[ { "id": "P10244-1.577.577", "start_pos": 577, "end_pos": 577, "uniprot_canonical_ac": "P10244-1", "length": 700, "uniprot_id": "MYBB_HUMAN", "protein_name": "Myb-related protein B", "refseq_ac": "NP_001265539", "refseq_name": "myb-related protein B isoform 2", "gene_name": "MYBL2", "gene_names_uniprotkb": "MYBL2; BMYB", "gene_names_refseq": "B-MYB; BMYB; MYBL2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P10244", "url": "https://www.uniprot.org/uniprotkb/P10244" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The cell-cycle regulated transcription factor B-Myb is phosphorylated by cyclin A/Cdk2 at sites that enhance its transactivation properties.", "journal": "Oncogene", "date": "1998", "authors": "Saville MK, Watson RJ", "evidence": [ { "database": "UniProtKB", "id": "P10244", "url": "https://www.uniprot.org/uniprotkb/P10244" }, { "database": "iPTMnet", "id": "P10244-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P10244-1" } ], "reference": [ { "type": "PubMed", "id": "9840932", "url": "https://glygen.org/publication/PubMed/9840932" } ] }, { "title": "Phosphorylation of B-Myb regulates its transactivation potential and DNA binding.", "journal": "The Journal of biological chemistry", "date": "1999", "authors": "Johnson TK, Schweppe RE, Septer J, Lewis RE", "evidence": [ { "database": "iPTMnet", "id": "P10244-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P10244-1" } ], "reference": [ { "type": "PubMed", "id": "10593981", "url": "https://glygen.org/publication/PubMed/10593981" } ] }, { "title": "B-Myb switches from Cyclin/Cdk-dependent to Jnk- and p38 kinase-dependent phosphorylation and associates with SC35 bodies after UV stress.", "journal": "Cell death & disease", "date": "2013", "authors": "Werwein E, Dzuganova M, Usadel C, Klempnauer KH", "evidence": [ { "database": "iPTMnet", "id": "P10244", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P10244" } ], "reference": [ { "type": "PubMed", "id": "23449447", "url": "https://glygen.org/publication/PubMed/23449447" } ] }, { "title": "Intramolecular interaction of B-MYB is regulated through Ser-577 phosphorylation.", "journal": "FEBS letters", "date": "2020-12", "authors": "Werwein Eugen, Biyanee Abhiruchi, Klempnauer Karl-Heinz", "evidence": [ { "database": "iPTMnet", "id": "P10244", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P10244" } ], "reference": [ { "type": "PubMed", "id": "32979888", "url": "https://glygen.org/publication/PubMed/32979888" } ] }, { "title": "Identification of cyclin A/Cdk2 phosphorylation sites in B-Myb.", "journal": "European journal of biochemistry", "date": "1999", "authors": "Bartsch O, Horstmann S, Toprak K, Klempnauer KH, Ferrari S", "evidence": [ { "database": "UniProtKB", "id": "P10244", "url": "https://www.uniprot.org/uniprotkb/P10244" }, { "database": "iPTMnet", "id": "P10244-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P10244-1" } ], "reference": [ { "type": "PubMed", "id": "10095772", "url": "https://glygen.org/publication/PubMed/10095772" } ] } ], "crossref": [ { "id": "P10244", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P10244", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "9840932", "url": "https://glygen.org/publication/PubMed/9840932", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P10244", "url": "https://www.uniprot.org/uniprotkb/P10244", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "10593981", "url": "https://glygen.org/publication/PubMed/10593981", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23449447", "url": "https://glygen.org/publication/PubMed/23449447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32979888", "url": "https://glygen.org/publication/PubMed/32979888", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10095772", "url": "https://glygen.org/publication/PubMed/10095772", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LIIEDDIRPEKQKRKPGLRR", "down_seq": "PIKKVRKSLALDIVDEDVKL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P24941-1", "kinase_gene_name": "CDK2", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P10244", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P10244" }, { "database": "PubMed", "id": "9840932", "url": "https://glygen.org/publication/PubMed/9840932" } ], "site_lbl": "Ser577" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by CDK2", "evidence": [ { "database": "UniProtKB", "id": "P10244", "url": "https://www.uniprot.org/uniprotkb/P10244" }, { "database": "iPTMnet", "id": "P10244", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P10244" }, { "database": "PubMed", "id": "10593981", "url": "https://glygen.org/publication/PubMed/10593981" }, { "database": "PubMed", "id": "23449447", "url": "https://glygen.org/publication/PubMed/23449447" }, { "database": "PubMed", "id": "32979888", "url": "https://glygen.org/publication/PubMed/32979888" }, { "database": "PubMed", "id": "9840932", "url": "https://glygen.org/publication/PubMed/9840932" }, { "database": "PubMed", "id": "10095772", "url": "https://glygen.org/publication/PubMed/10095772" } ], "site_lbl": "Ser577" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "607", "end_pos": "607" } ] }, { "type": "snv", "site_list": [ { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "627", "end_pos": "627" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "695", "end_pos": "695" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "241", "end_pos": "241" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "600", "end_pos": "600" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P10244-1.600.600", "start_pos": 600, "end_pos": 600, "uniprot_canonical_ac": "P10244-1", "length": 700, "uniprot_id": "MYBB_HUMAN", "protein_name": "Myb-related protein B", "refseq_ac": "NP_001265539", "refseq_name": "myb-related protein B isoform 2", "gene_name": "MYBL2", "gene_names_uniprotkb": "MYBL2; BMYB", "gene_names_refseq": "B-MYB; BMYB; MYBL2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P10244", "url": "https://www.uniprot.org/uniprotkb/P10244" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "UniProtKB", "id": "P10244", "url": "https://www.uniprot.org/uniprotkb/P10244" }, { "database": "iPTMnet", "id": "P10244-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P10244-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P10244", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P10244", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KKVRKSLALDIVDEDVKLMM", "down_seq": "TLPKSLSLPTTAPSNSSSLT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P10244", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P10244" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser600" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "607", "end_pos": "607" } ] }, { "type": "snv", "site_list": [ { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "438", "end_pos": "438" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "627", "end_pos": "627" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "695", "end_pos": "695" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "241", "end_pos": "241" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "505", "end_pos": "505" }, { "start_pos": "515", "end_pos": "515" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "600", "end_pos": "600" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P10244-1.607.607", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O14656-1.143.143", "start_pos": 143, "end_pos": 143, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Torsin A and its torsion dystonia-associated mutant forms are lumenal glycoproteins that exhibit distinct subcellular localizations.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "Kustedjo K, Bracey MH, Cravatt BF", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656#ptm_processing" }, { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "reference": [ { "type": "PubMed", "id": "10871631", "url": "https://glygen.org/publication/PubMed/10871631" } ] } ], "crossref": [ { "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "10871631", "url": "https://glygen.org/publication/PubMed/10871631", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs2031210990", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2031210990", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2031210990", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2031210990#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "O14656", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14656", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs937984745", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs937984745", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs937984745", "url": "https://www.ensembl.org/id/rs937984745", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GLNSDYVHLFVATLHFPHAS", "down_seq": "ITLYKDQLQLWIRGNVSACA", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "High mannose", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) (high mannose) asparagine;High mannose", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn143", "evidence": [ { "id": "O14656", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O14656#ptm_processing" }, { "id": "10871631", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/10871631" } ] } ], "mutagenesis": [ { "sequence_org": "N", "sequence_mut": "Q", "comment": "Reduces N-glycosylation.", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" }, { "database": "PubMed", "id": "10871631", "url": "https://glygen.org/publication/PubMed/10871631" } ] } ], "snv": [ { "evidence": [ { "id": "rs2031210990", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2031210990" }, { "id": "rs2031210990", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2031210990#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NIT->DIT).", "chr_id": "9", "chr_pos": "129822598", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N143", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "O14656", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14656" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NIT->HIT).", "chr_id": "9", "chr_pos": "129822598", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N143", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs937984745", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs937984745" }, { "id": "rs937984745", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs937984745" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NIT->IIT).", "chr_id": "9", "chr_pos": "129822597", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N143", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O14656-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O14656-1.158.158", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "O14656-1.160.160", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O14656-1.158.158", "start_pos": 158, "end_pos": 158, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "1821", "url": "https://glyconnect.expasy.org/browser/proteins/1821" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "title": "Torsin A and its torsion dystonia-associated mutant forms are lumenal glycoproteins that exhibit distinct subcellular localizations.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "Kustedjo K, Bracey MH, Cravatt BF", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656#ptm_processing" }, { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "reference": [ { "type": "PubMed", "id": "10871631", "url": "https://glygen.org/publication/PubMed/10871631" } ] }, { "title": "N-linked glycosylation enrichment for in-depth cell surface proteomics of diffuse large B-cell lymphoma subtypes.", "journal": "Molecular & cellular proteomics : MCP", "date": "2014", "authors": "Deeb SJ, Cox J, Schmidt-Supprian M, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1821", "url": "https://glyconnect.expasy.org/browser/proteins/1821", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "10871631", "url": "https://glygen.org/publication/PubMed/10871631", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs774198905", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774198905", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774198905", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774198905", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774198905", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774198905#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774198905", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774198905", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs747755961", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747755961", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747755961", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747755961", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747755961", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747755961", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FPHASNITLYKDQLQLWIRG", "down_seq": "VSACARSIFIFDEMDKMHAG", "glycosylation": [ { "glytoucan_ac": "G02815KT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GnVSACAR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn158", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G06110VR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn158", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1821", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1821" } ] }, { "glytoucan_ac": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GnVSACAR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn158", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G41247ZX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GnVSACAR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn158", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GnVSACAR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn158", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70101JE", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn158", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1821", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1821" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GnVSACAR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn158", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G92050GC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GnVSACAR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn158", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn158", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "O14656", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O14656#ptm_processing" }, { "id": "10871631", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/10871631" }, { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "mutagenesis": [ { "sequence_org": "N", "sequence_mut": "Q", "comment": "Reduces N-glycosylation.", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" }, { "database": "PubMed", "id": "10871631", "url": "https://glygen.org/publication/PubMed/10871631" } ] } ], "snv": [ { "evidence": [ { "id": "rs774198905", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774198905" }, { "id": "rs774198905", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774198905" }, { "id": "rs774198905", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774198905#frequency_tab" }, { "id": "rs774198905", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774198905" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVS->KVS).", "chr_id": "9", "chr_pos": "129818891", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N158", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs747755961", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747755961" }, { "id": "rs747755961", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747755961" }, { "id": "rs747755961", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747755961" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVS->SVS).", "chr_id": "9", "chr_pos": "129818892", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N158", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "O14656-1.143.143", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "O14656-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O14656-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "O14656-1.171.171", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 9 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 8 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 8 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 8 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 8 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 8 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O14656-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Synthesis of a Highly Azide-Reactive and Thermosensitive Biofunctional Reagent for Efficient Enrichment and Large-Scale Identification of O-GlcNAc Proteins by Mass Spectrometry.", "journal": "Analytical chemistry", "date": "2017", "authors": "Zhang W, Liu T, Dong H, Bai H, Tian F, Shi Z, Chen M, Wang J, Qin W, Qian X", "evidence": [ { "database": "O-GlcNAc Database", "id": "O14656", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O14656" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Genetic manipulation of OGT enhances NK cell-mediated cytotoxicity in tumor immunity.", "journal": "Journal of advanced research", "date": "2025-09-04", "authors": "Oh Se-Chan, Jeon Bong Chan, Jang In-Hwan, Song Mi-Ran, Hwang Heeyoun, An Dasom, Yue Liu, Jung Yuri, Lee Yunhee, Jo Seona, Park Sung-Kyun, Kim Tae-Don", "evidence": [ { "database": "O-GlcNAc Database", "id": "O14656", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O14656" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "title": "FBXO31-mediated ubiquitination of OGT maintains O-GlcNAcylation homeostasis to restrain endometrial malignancy.", "journal": "Nature communications", "date": "2025-02-02", "authors": "Zhang Na, Meng Yang, Mao Song, Ni Huiling, Huang Canhua, Shen Licong, Fu Kun, Lv Lu, Yu Chunhong, Meekrathok Piyanat, Kuang Chunmei, Chen Fang, Zhang Yu, Yuan Kai", "evidence": [ { "database": "O-GlcNAc Database", "id": "O14656", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O14656" } ], "reference": [ { "type": "PubMed", "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "O14656", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O14656" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O14656", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O14656", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "O14656", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O14656" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "39894887", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39894887" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "O14656-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O14656-1.20.20", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O14656-1.108.108", "start_pos": 108, "end_pos": 108, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Effect of torsinA on membrane proteins reveals a loss of function and a dominant-negative phenotype of the dystonia-associated DeltaE-torsinA mutant.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2004", "authors": "Torres GE, Sweeney AL, Beaulieu JM, Shashidharan P, Caron MG", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "reference": [ { "type": "PubMed", "id": "15505207", "url": "https://glygen.org/publication/PubMed/15505207" } ] }, { "title": "Printor, a novel torsinA-interacting protein implicated in dystonia pathogenesis.", "journal": "The Journal of biological chemistry", "date": "2009", "authors": "Giles LM, Li L, Chin LS", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "reference": [ { "type": "PubMed", "id": "19535332", "url": "https://glygen.org/publication/PubMed/19535332" } ] }, { "title": "LULL1 retargets TorsinA to the nuclear envelope revealing an activity that is impaired by the DYT1 dystonia mutation.", "journal": "Molecular biology of the cell", "date": "2009", "authors": "Vander Heyden AB, Naismith TV, Snapp EL, Hodzic D, Hanson PI", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "reference": [ { "type": "PubMed", "id": "19339278", "url": "https://glygen.org/publication/PubMed/19339278" } ] } ], "crossref": [ { "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15505207", "url": "https://glygen.org/publication/PubMed/15505207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19535332", "url": "https://glygen.org/publication/PubMed/19535332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19339278", "url": "https://glygen.org/publication/PubMed/19339278", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "NNPKPKKPLTLSLHGWTGTG", "down_seq": "NFVSKIIAENIYEGGLNSDY", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "A", "comment": "Loss of ATP-binding. No effect on interaction with KLHL14. Increases interaction with TOR1AIP1 and TOR1AIP2. Abolishes interaction with SLC6A3.", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" }, { "database": "PubMed", "id": "15505207", "url": "https://glygen.org/publication/PubMed/15505207" }, { "database": "PubMed", "id": "19535332", "url": "https://glygen.org/publication/PubMed/19535332" }, { "database": "PubMed", "id": "19339278", "url": "https://glygen.org/publication/PubMed/19339278" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "O14656-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O14656-1.111.111", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O14656-1.171.171", "start_pos": 171, "end_pos": 171, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Relative tissue expression of homologous torsinB correlates with the neuronal specific importance of DYT1 dystonia-associated torsinA.", "journal": "Human molecular genetics", "date": "2010", "authors": "Jungwirth M, Dear ML, Brown P, Holbrook K, Goodchild R", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "reference": [ { "type": "PubMed", "id": "20015956", "url": "https://glygen.org/publication/PubMed/20015956" } ] }, { "title": "Regulation of Torsin ATPases by LAP1 and LULL1.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2013", "authors": "Zhao C, Brown RS, Chase AR, Eisele MR, Schlieker C", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "reference": [ { "type": "PubMed", "id": "23569223", "url": "https://glygen.org/publication/PubMed/23569223" } ] }, { "title": "Printor, a novel torsinA-interacting protein implicated in dystonia pathogenesis.", "journal": "The Journal of biological chemistry", "date": "2009", "authors": "Giles LM, Li L, Chin LS", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "reference": [ { "type": "PubMed", "id": "19535332", "url": "https://glygen.org/publication/PubMed/19535332" } ] }, { "title": "Structures of TorsinA and its disease-mutant complexed with an activator reveal the molecular basis for primary dystonia.", "journal": "eLife", "date": "2016", "authors": "Demircioglu FE, Sosa BA, Ingram J, Ploegh HL, Schwartz TU", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "reference": [ { "type": "PubMed", "id": "27490483", "url": "https://glygen.org/publication/PubMed/27490483" } ] }, { "title": "LULL1 retargets TorsinA to the nuclear envelope revealing an activity that is impaired by the DYT1 dystonia mutation.", "journal": "Molecular biology of the cell", "date": "2009", "authors": "Vander Heyden AB, Naismith TV, Snapp EL, Hodzic D, Hanson PI", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "reference": [ { "type": "PubMed", "id": "19339278", "url": "https://glygen.org/publication/PubMed/19339278" } ] } ], "crossref": [ { "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20015956", "url": "https://glygen.org/publication/PubMed/20015956", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23569223", "url": "https://glygen.org/publication/PubMed/23569223", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19535332", "url": "https://glygen.org/publication/PubMed/19535332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27490483", "url": "https://glygen.org/publication/PubMed/27490483", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19339278", "url": "https://glygen.org/publication/PubMed/19339278", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "LQLWIRGNVSACARSIFIFD", "down_seq": "MDKMHAGLIDAIKPFLDYYD", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "Q", "comment": "Loss of ATP hydrolysis. Loss of interaction with KLHL14. Localizes in the nuclear envelope. No effect on interaction with TOR1AIP1.", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" }, { "database": "PubMed", "id": "20015956", "url": "https://glygen.org/publication/PubMed/20015956" }, { "database": "PubMed", "id": "23569223", "url": "https://glygen.org/publication/PubMed/23569223" }, { "database": "PubMed", "id": "19535332", "url": "https://glygen.org/publication/PubMed/19535332" }, { "database": "PubMed", "id": "27490483", "url": "https://glygen.org/publication/PubMed/27490483" }, { "database": "PubMed", "id": "19339278", "url": "https://glygen.org/publication/PubMed/19339278" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "O14656-1.158.158", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "O14656-1.160.160", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O14656-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Biosynthesis of the dystonia-associated AAA+ ATPase torsinA at the endoplasmic reticulum.", "journal": "The Biochemical journal", "date": "2007", "authors": "Callan AC, Bunning S, Jones OT, High S, Swanton E", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "reference": [ { "type": "PubMed", "id": "17037984", "url": "https://glygen.org/publication/PubMed/17037984" } ] } ], "crossref": [ { "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17037984", "url": "https://glygen.org/publication/PubMed/17037984", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "MKLGRAVLGLLLLAPSV", "down_seq": "QAVEPISLGLALAGVLTGYI", "mutagenesis": [ { "sequence_org": "V", "sequence_mut": "F", "comment": "Inhibits sequence signal cleavage.", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" }, { "database": "PubMed", "id": "17037984", "url": "https://glygen.org/publication/PubMed/17037984" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "O14656-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O14656-1.20.20", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O14656-1.33.33", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O14656-1.20.20", "start_pos": 20, "end_pos": 20, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Biosynthesis of the dystonia-associated AAA+ ATPase torsinA at the endoplasmic reticulum.", "journal": "The Biochemical journal", "date": "2007", "authors": "Callan AC, Bunning S, Jones OT, High S, Swanton E", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "reference": [ { "type": "PubMed", "id": "17037984", "url": "https://glygen.org/publication/PubMed/17037984" } ] } ], "crossref": [ { "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17037984", "url": "https://glygen.org/publication/PubMed/17037984", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "", "down_seq": "VEPISLGLALAGVLTGYIYP", "mutagenesis": [ { "sequence_org": "A", "sequence_mut": "F", "comment": "Inhibits sequence signal cleavage.", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" }, { "database": "PubMed", "id": "17037984", "url": "https://glygen.org/publication/PubMed/17037984" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O14656-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O14656-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "O14656-1.33.33", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O14656-1.33.33", "start_pos": 33, "end_pos": 33, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Biosynthesis of the dystonia-associated AAA+ ATPase torsinA at the endoplasmic reticulum.", "journal": "The Biochemical journal", "date": "2007", "authors": "Callan AC, Bunning S, Jones OT, High S, Swanton E", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "reference": [ { "type": "PubMed", "id": "17037984", "url": "https://glygen.org/publication/PubMed/17037984" } ] } ], "crossref": [ { "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17037984", "url": "https://glygen.org/publication/PubMed/17037984", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LAPSVVQAVEPISLGLALAG", "down_seq": "LTGYIYPRLYCLFAECCGQK", "mutagenesis": [ { "sequence_org": "V", "sequence_mut": "N", "comment": "N-glycosylated.", "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" }, { "database": "PubMed", "id": "17037984", "url": "https://glygen.org/publication/PubMed/17037984" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "O14656-1.18.18", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "O14656-1.20.20", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O14656-1.107.107", "start_pos": 107, "end_pos": 107, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O14656", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14656", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "INNPKPKKPLTLSLHGWTGT", "down_seq": "KNFVSKIIAENIYEGGLNSD", "snv": [ { "evidence": [ { "id": "O14656", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14656" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "129822705", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G107", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "O14656-1.108.108", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O14656-1.111.111", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O14656-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O14656", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14656", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "KPKKPLTLSLHGWTGTGKNF", "down_seq": "SKIIAENIYEGGLNSDYVHL", "snv": [ { "evidence": [ { "id": "O14656", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14656" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "129822694", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V111", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "O14656-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O14656-1.108.108", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O14656-1.145.145", "start_pos": 145, "end_pos": 145, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2031210712", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2031210712", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2031210712", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2031210712", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "O14656", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14656", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NSDYVHLFVATLHFPHASNI", "down_seq": "LYKDQLQLWIRGNVSACARS", "snv": [ { "evidence": [ { "id": "rs2031210712", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2031210712" }, { "id": "rs2031210712", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2031210712" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NIT->NIA).", "chr_id": "9", "chr_pos": "129822592", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T145", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "O14656", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14656" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NIT->NII).", "chr_id": "9", "chr_pos": "129822591", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T145", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O14656-1.143.143", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "O14656-1.158.158", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O14656-1.160.160", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O14656-1.160.160", "start_pos": 160, "end_pos": 160, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs746315862", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746315862", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746315862", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746315862", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs746315862", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746315862", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HASNITLYKDQLQLWIRGNV", "down_seq": "ACARSIFIFDEMDKMHAGLI", "snv": [ { "evidence": [ { "id": "rs746315862", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746315862" }, { "id": "rs746315862", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746315862" }, { "id": "rs746315862", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746315862" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVS->NVR).", "chr_id": "9", "chr_pos": "129818885", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S160", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "O14656-1.143.143", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "O14656-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O14656-1.158.158", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "O14656-1.171.171", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O14656-1.210.210", "start_pos": 210, "end_pos": 210, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1353009976", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1353009976", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1353009976", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1353009976#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1353009976", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1353009976", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "YDLVDGVSYQKAMFIFLSNA", "down_seq": "AERITDVALDFWRSGKQRED", "snv": [ { "evidence": [ { "id": "rs1353009976", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1353009976" }, { "id": "rs1353009976", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1353009976#frequency_tab" }, { "id": "rs1353009976", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1353009976" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NAG->NAS).", "chr_id": "9", "chr_pos": "129818833", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G210", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O14656-1.248.248", "start_pos": 248, "end_pos": 248, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753511091", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753511091", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753511091", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753511091", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753511091", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753511091#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs753511091", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753511091", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "REDIKLKDIEHALSVSVFNN", "down_seq": "NSGFWHSSLIDRNLIDYFVP", "snv": [ { "evidence": [ { "id": "rs753511091", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753511091" }, { "id": "rs753511091", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753511091" }, { "id": "rs753511091", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753511091#frequency_tab" }, { "id": "rs753511091", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753511091" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KNS->NNS).", "chr_id": "9", "chr_pos": "129818524", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K248", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "O14656-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O14656-1.263.263", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O14656-1.249.249", "start_pos": 249, "end_pos": 249, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2031097850", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2031097850", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2031097850", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2031097850#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2031097850", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2031097850", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "EDIKLKDIEHALSVSVFNNK", "down_seq": "SGFWHSSLIDRNLIDYFVPF", "snv": [ { "evidence": [ { "id": "rs2031097850", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2031097850" }, { "id": "rs2031097850", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2031097850#frequency_tab" }, { "id": "rs2031097850", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2031097850" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKN->NKT).", "chr_id": "9", "chr_pos": "129818522", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N249", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "O14656-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O14656-1.263.263", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O14656-1.263.263", "start_pos": 263, "end_pos": 263, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs748013566", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748013566", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748013566", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748013566", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748013566", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748013566#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs748013566", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748013566", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "SVFNNKNSGFWHSSLIDRNL", "down_seq": "DYFVPFLPLEYKHLKMCIRV", "snv": [ { "evidence": [ { "id": "rs748013566", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748013566" }, { "id": "rs748013566", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748013566" }, { "id": "rs748013566", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748013566#frequency_tab" }, { "id": "rs748013566", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748013566" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLI->NLT).", "chr_id": "9", "chr_pos": "129814183", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I263", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "O14656-1.248.248", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "O14656-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O14656-1.278.278", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O14656-1.278.278", "start_pos": 278, "end_pos": 278, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1285711883", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1285711883", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1285711883", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1285711883#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1285711883", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1285711883", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "IDRNLIDYFVPFLPLEYKHL", "down_seq": "MCIRVEMQSRGYEIDEDIVS", "snv": [ { "evidence": [ { "id": "rs1285711883", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1285711883" }, { "id": "rs1285711883", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1285711883#frequency_tab" }, { "id": "rs1285711883", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1285711883" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KMC->NMC).", "chr_id": "9", "chr_pos": "129814137", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K278", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "O14656-1.263.263", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O14656-1.82.82", "start_pos": 82, "end_pos": 82, "uniprot_canonical_ac": "O14656-1", "length": 332, "uniprot_id": "TOR1A_HUMAN", "protein_name": "Torsin-1A", "refseq_ac": "NP_000104", "refseq_name": "torsin-1A precursor", "gene_name": "TOR1A", "gene_names_uniprotkb": "TOR1A; DQ2; DYT1; TA; TORA", "gene_names_refseq": "AMC5; DQ2; DYT1; TOR1A", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O14656", "url": "https://www.uniprot.org/uniprotkb/O14656" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O14656", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14656", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QKDLDDNLFGQHLAKKIILN", "down_seq": "VFGFINNPKPKKPLTLSLHG", "snv": [ { "evidence": [ { "id": "O14656", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O14656" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "129822780", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A82", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "18", "end_pos": "18" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "snv", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "248", "end_pos": "248" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "82", "end_pos": "82" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O96014-1.160.160", "start_pos": 160, "end_pos": 160, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1399310579", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1399310579", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1399310579", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1399310579", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "CGPVPGEPPGPGNRWGGCAD", "down_seq": "LSYGLLMGAKFSDAPMKVKK", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn160", "evidence": [ { "id": "O96014", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O96014#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1399310579", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1399310579" }, { "id": "rs1399310579", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1399310579" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLS->SLS).", "chr_id": "11", "chr_pos": "76194685", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N160", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O96014-1.162.162", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O96014-1.300.300", "start_pos": 300, "end_pos": 300, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1953111147", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1953111147", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1953111147", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1953111147#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "PDFCMKNEKVGSHGTQDRQC", "down_seq": "KTSNGSDSCDLMCCGRGYNP", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn300", "evidence": [ { "id": "O96014", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O96014#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1953111147", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1953111147" }, { "id": "rs1953111147", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1953111147#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKT->YKT).", "chr_id": "11", "chr_pos": "76187232", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N300", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O96014-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "O96014-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O96014-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O96014-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O96014-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O96014-1.307.307", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O96014-1.304.304", "start_pos": 304, "end_pos": 304, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "MKNEKVGSHGTQDRQCNKTS", "down_seq": "GSDSCDLMCCGRGYNPYTDR", "glycosylation": [ { "glytoucan_ac": "G83460ZZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "TSNGSDSCDLMCCGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn304", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn304", "evidence": [ { "id": "O96014", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O96014#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "O96014-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "O96014-1.300.300", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O96014-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O96014-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O96014-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O96014-1.324.324", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O96014-1.40.40", "start_pos": 40, "end_pos": 40, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "O96014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1591306885", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1591306885", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1591306885", "url": "https://www.ensembl.org/id/rs1591306885", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GVCYGIKWLALSKTPSALAL", "down_seq": "QTQHCKQLEGLVSAQVQLCR", "glycosylation": [ { "glytoucan_ac": "G83460ZZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "TPSALALNQTQHCK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn40", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn40", "evidence": [ { "id": "O96014", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O96014#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "O96014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NQT->DQT).", "chr_id": "11", "chr_pos": "76196684", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N40", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1591306885", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1591306885" }, { "id": "rs1591306885", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1591306885" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NQT->TQT).", "chr_id": "11", "chr_pos": "76196683", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N40", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O96014-1.42.42", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O96014-1.90.90", "start_pos": 90, "end_pos": 90, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "VHAAREVMKACRRAFADMRW", "down_seq": "CSSIELAPNYLLDLERGTRE", "glycosylation": [ { "glytoucan_ac": "G93910IH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "WNCSSIELAPNYLLDLER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn90", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn90", "evidence": [ { "id": "O96014", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O96014#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "O96014-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O96014-1.92.92", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O96014-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O96014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs200871564", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200871564", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200871564", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200871564", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200871564", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200871564#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200871564", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200871564", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs200871564", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200871564", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "CYGIKWLALSKTPSALALNQ", "down_seq": "QHCKQLEGLVSAQVQLCRSN", "snv": [ { "evidence": [ { "id": "O96014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014" }, { "id": "rs200871564", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200871564" }, { "id": "rs200871564", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200871564" }, { "id": "rs200871564", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200871564#frequency_tab" }, { "id": "rs200871564", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200871564" }, { "id": "rs200871564", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200871564" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "606", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); n-glyco-sequon-loss (NQT->NQM).", "chr_id": "11", "chr_pos": "76196677", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T42", "disease": [ { "disease_id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid cancer", "description": "An endocrine gland cancer located in the thyroid gland located in the neck below the thyroid cartilage." }, "synonyms": [ { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "Thyroid gland neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant tumour of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid gland cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3973", "DOID:0080524", "DOID:0080525" ], "evidence": [ { "id": "1781", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1781" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O96014-1.40.40", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O96014-1.127.127", "start_pos": 127, "end_pos": 127, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O96014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GTRESAFVYALSAAAISHAI", "down_seq": "RACTSGDLPGCSCGPVPGEP", "snv": [ { "evidence": [ { "id": "O96014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "76194784", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A127", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O96014-1.162.162", "start_pos": 162, "end_pos": 162, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1315047010", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1315047010", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1315047010", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1315047010#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1315047010", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1315047010", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PVPGEPPGPGNRWGGCADNL", "down_seq": "YGLLMGAKFSDAPMKVKKTG", "snv": [ { "evidence": [ { "id": "rs1315047010", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1315047010" }, { "id": "rs1315047010", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1315047010#frequency_tab" }, { "id": "rs1315047010", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1315047010" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLS->NLG).", "chr_id": "11", "chr_pos": "76194680", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S162", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O96014-1.160.160", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O96014-1.221.221", "start_pos": 221, "end_pos": 221, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O96014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LRASLEMKCKCHGVSGSCSI", "down_seq": "TCWKGLQELQDVAADLKTRY", "snv": [ { "evidence": [ { "id": "O96014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "11", "chr_pos": "76191793", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R221", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O96014-1.250.250", "start_pos": 250, "end_pos": 250, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O96014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LQDVAADLKTRYLSATKVVH", "down_seq": "PMGTRKHLVPKDLDIRPVKD", "snv": [ { "evidence": [ { "id": "O96014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "76191706", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R250", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "O96014-1.269.269", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O96014-1.269.269", "start_pos": 269, "end_pos": 269, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O96014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs746907143", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746907143", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746907143", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746907143", "database": "ExAC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "HRPMGTRKHLVPKDLDIRPV", "down_seq": "DSELVYLQSSPDFCMKNEKV", "snv": [ { "evidence": [ { "id": "O96014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014" }, { "id": "rs746907143", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746907143" }, { "id": "rs746907143", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746907143" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KDS->NDS).", "chr_id": "11", "chr_pos": "76191647", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K269", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O96014-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O96014-1.281.281", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O96014-1.281.281", "start_pos": 281, "end_pos": 281, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs751885211", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751885211", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751885211", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751885211", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751885211", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751885211", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KDLDIRPVKDSELVYLQSSP", "down_seq": "FCMKNEKVGSHGTQDRQCNK", "snv": [ { "evidence": [ { "id": "rs751885211", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751885211" }, { "id": "rs751885211", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751885211" }, { "id": "rs751885211", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751885211" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DFC->NFC).", "chr_id": "11", "chr_pos": "76191613", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D281", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "O96014-1.269.269", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "O96014-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "O96014-1.300.300", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O96014-1.301.301", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O96014-1.292.292", "start_pos": 292, "end_pos": 292, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O96014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "ELVYLQSSPDFCMKNEKVGS", "down_seq": "GTQDRQCNKTSNGSDSCDLM", "snv": [ { "evidence": [ { "id": "O96014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (HGT->NGT).", "chr_id": "11", "chr_pos": "76191580", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H292", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "O96014-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "O96014-1.300.300", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O96014-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O96014-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O96014-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O96014-1.307.307", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O96014-1.301.301", "start_pos": 301, "end_pos": 301, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O96014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1021925005", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1021925005", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1021925005", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1021925005#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1021925005", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1021925005", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "DFCMKNEKVGSHGTQDRQCN", "down_seq": "TSNGSDSCDLMCCGRGYNPY", "snv": [ { "evidence": [ { "id": "O96014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014" }, { "id": "rs1021925005", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1021925005" }, { "id": "rs1021925005", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1021925005#frequency_tab" }, { "id": "rs1021925005", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1021925005" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KTS->NTS).", "chr_id": "11", "chr_pos": "76187227", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K301", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O96014-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "O96014-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O96014-1.300.300", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O96014-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O96014-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O96014-1.307.307", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O96014-1.306.306", "start_pos": 306, "end_pos": 306, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs775912689", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775912689", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775912689", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775912689", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775912689", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775912689#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs775912689", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775912689", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NEKVGSHGTQDRQCNKTSNG", "down_seq": "DSCDLMCCGRGYNPYTDRVV", "snv": [ { "evidence": [ { "id": "rs775912689", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775912689" }, { "id": "rs775912689", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775912689" }, { "id": "rs775912689", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775912689#frequency_tab" }, { "id": "rs775912689", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775912689" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NGS->NGR).", "chr_id": "11", "chr_pos": "76187212", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S306", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O96014-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O96014-1.300.300", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O96014-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O96014-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O96014-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "O96014-1.324.324", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O96014-1.307.307", "start_pos": 307, "end_pos": 307, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs770136447", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770136447", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770136447", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770136447", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs770136447", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770136447#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs770136447", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770136447", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "EKVGSHGTQDRQCNKTSNGS", "down_seq": "SCDLMCCGRGYNPYTDRVVE", "snv": [ { "evidence": [ { "id": "rs770136447", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770136447" }, { "id": "rs770136447", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770136447" }, { "id": "rs770136447", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770136447#frequency_tab" }, { "id": "rs770136447", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770136447" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DSC->NSC).", "chr_id": "11", "chr_pos": "76187211", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D307", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "O96014-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "O96014-1.300.300", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O96014-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O96014-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O96014-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "O96014-1.324.324", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O96014-1.324.324", "start_pos": 324, "end_pos": 324, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O96014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "NGSDSCDLMCCGRGYNPYTD", "down_seq": "VVERCHCKYHWCCYVTCRRC", "snv": [ { "evidence": [ { "id": "O96014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "76187160", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R324", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O96014-1.304.304", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "O96014-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "O96014-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O96014-1.334.334", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O96014-1.334.334", "start_pos": 334, "end_pos": 334, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1953108552", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1953108552", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1953108552", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1953108552#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "CGRGYNPYTDRVVERCHCKY", "down_seq": "WCCYVTCRRCERTVERYVCK", "snv": [ { "evidence": [ { "id": "rs1953108552", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1953108552" }, { "id": "rs1953108552", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1953108552#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HWC->NWC).", "chr_id": "11", "chr_pos": "76187130", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H334", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "O96014-1.324.324", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O96014-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1277702831", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1277702831", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1277702831", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1277702831", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LCRSNLELMHTVVHAAREVM", "down_seq": "ACRRAFADMRWNCSSIELAP", "snv": [ { "evidence": [ { "id": "rs1277702831", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1277702831" }, { "id": "rs1277702831", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1277702831" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KAC->NAC).", "chr_id": "11", "chr_pos": "76196568", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K78", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "O96014-1.90.90", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O96014-1.92.92", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O96014-1.92.92", "start_pos": 92, "end_pos": 92, "uniprot_canonical_ac": "O96014-1", "length": 354, "uniprot_id": "WNT11_HUMAN", "protein_name": "Protein Wnt-11", "refseq_ac": "NP_004617", "refseq_name": "protein Wnt-11 precursor", "gene_name": "WNT11", "gene_names_uniprotkb": "WNT11", "gene_names_refseq": "HWNT11; WNT11", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O96014", "url": "https://www.uniprot.org/uniprotkb/O96014" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O96014", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AAREVMKACRRAFADMRWNC", "down_seq": "SIELAPNYLLDLERGTRESA", "snv": [ { "evidence": [ { "id": "O96014", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O96014" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NCS->NCF).", "chr_id": "11", "chr_pos": "76196527", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S92", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "160", "end_pos": "160" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "snv", "site_list": [ { "start_pos": "42", "end_pos": "42" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "92", "end_pos": "92" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O96014-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O96014-1.90.90", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96N58-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q96N58-1", "length": 590, "uniprot_id": "ZN578_HUMAN", "protein_name": "Zinc finger protein 578", "refseq_ac": "NP_001093164", "refseq_name": "zinc finger protein 578", "gene_name": "ZNF578", "gene_names_uniprotkb": "ZNF578", "gene_names_refseq": "ZNF578", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96N58", "url": "https://www.uniprot.org/uniprotkb/Q96N58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q96N58", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96N58" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "crossref": [ { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96N58", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96N58", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q96N58", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96N58" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "584", "end_pos": "584" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96N58-1.211.211", "start_pos": 211, "end_pos": 211, "uniprot_canonical_ac": "Q96N58-1", "length": 590, "uniprot_id": "ZN578_HUMAN", "protein_name": "Zinc finger protein 578", "refseq_ac": "NP_001093164", "refseq_name": "zinc finger protein 578", "gene_name": "ZNF578", "gene_names_uniprotkb": "ZNF578", "gene_names_refseq": "ZNF578", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96N58", "url": "https://www.uniprot.org/uniprotkb/Q96N58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96N58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "STSQRISCRPETHTPNNYGN", "down_seq": "FFHSSLLTQKQEVHMREKSF", "snv": [ { "evidence": [ { "id": "Q96N58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "52511013", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "N211", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "584", "end_pos": "584" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96N58-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "Q96N58-1", "length": 590, "uniprot_id": "ZN578_HUMAN", "protein_name": "Zinc finger protein 578", "refseq_ac": "NP_001093164", "refseq_name": "zinc finger protein 578", "gene_name": "ZNF578", "gene_names_uniprotkb": "ZNF578", "gene_names_refseq": "ZNF578", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96N58", "url": "https://www.uniprot.org/uniprotkb/Q96N58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96N58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IHLGEKQYKFDICGKVFNEK", "down_seq": "YLARHRRCHTSEKPYKCNEC", "snv": [ { "evidence": [ { "id": "Q96N58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "52511195", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R272", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "584", "end_pos": "584" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q96N58-1.276.276", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q96N58-1.283.283", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96N58-1.276.276", "start_pos": 276, "end_pos": 276, "uniprot_canonical_ac": "Q96N58-1", "length": 590, "uniprot_id": "ZN578_HUMAN", "protein_name": "Zinc finger protein 578", "refseq_ac": "NP_001093164", "refseq_name": "zinc finger protein 578", "gene_name": "ZNF578", "gene_names_uniprotkb": "ZNF578", "gene_names_refseq": "ZNF578", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96N58", "url": "https://www.uniprot.org/uniprotkb/Q96N58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96N58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EKQYKFDICGKVFNEKRYLA", "down_seq": "HRRCHTSEKPYKCNECGKSF", "snv": [ { "evidence": [ { "id": "Q96N58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "52511208", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R276", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "584", "end_pos": "584" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q96N58-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q96N58-1.283.283", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96N58-1.283.283", "start_pos": 283, "end_pos": 283, "uniprot_canonical_ac": "Q96N58-1", "length": 590, "uniprot_id": "ZN578_HUMAN", "protein_name": "Zinc finger protein 578", "refseq_ac": "NP_001093164", "refseq_name": "zinc finger protein 578", "gene_name": "ZNF578", "gene_names_uniprotkb": "ZNF578", "gene_names_refseq": "ZNF578", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96N58", "url": "https://www.uniprot.org/uniprotkb/Q96N58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96N58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ICGKVFNEKRYLARHRRCHT", "down_seq": "EKPYKCNECGKSFSYKSSLT", "snv": [ { "evidence": [ { "id": "Q96N58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4177", "subjects_positive": "8", "frequency": "0.2", "sequence_org": "S", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "52511228", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S283", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "584", "end_pos": "584" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q96N58-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q96N58-1.276.276", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96N58-1.306.306", "start_pos": 306, "end_pos": 306, "uniprot_canonical_ac": "Q96N58-1", "length": 590, "uniprot_id": "ZN578_HUMAN", "protein_name": "Zinc finger protein 578", "refseq_ac": "NP_001093164", "refseq_name": "zinc finger protein 578", "gene_name": "ZNF578", "gene_names_uniprotkb": "ZNF578", "gene_names_refseq": "ZNF578", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96N58", "url": "https://www.uniprot.org/uniprotkb/Q96N58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96N58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PYKCNECGKSFSYKSSLTCH", "down_seq": "RCHTGEKPYKCNECGKSFSY", "snv": [ { "evidence": [ { "id": "Q96N58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "52511298", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R306", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "584", "end_pos": "584" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q96N58-1.311.311", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96N58-1.311.311", "start_pos": 311, "end_pos": 311, "uniprot_canonical_ac": "Q96N58-1", "length": 590, "uniprot_id": "ZN578_HUMAN", "protein_name": "Zinc finger protein 578", "refseq_ac": "NP_001093164", "refseq_name": "zinc finger protein 578", "gene_name": "ZNF578", "gene_names_uniprotkb": "ZNF578", "gene_names_refseq": "ZNF578", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96N58", "url": "https://www.uniprot.org/uniprotkb/Q96N58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96N58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "ECGKSFSYKSSLTCHRRCHT", "down_seq": "EKPYKCNECGKSFSYKSSLT", "snv": [ { "evidence": [ { "id": "Q96N58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "4", "frequency": "0.2", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "19", "chr_pos": "52511312", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G311", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "584", "end_pos": "584" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q96N58-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q96N58-1.331.331", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96N58-1.331.331", "start_pos": 331, "end_pos": 331, "uniprot_canonical_ac": "Q96N58-1", "length": 590, "uniprot_id": "ZN578_HUMAN", "protein_name": "Zinc finger protein 578", "refseq_ac": "NP_001093164", "refseq_name": "zinc finger protein 578", "gene_name": "ZNF578", "gene_names_uniprotkb": "ZNF578", "gene_names_refseq": "ZNF578", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96N58", "url": "https://www.uniprot.org/uniprotkb/Q96N58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96N58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GEKPYKCNECGKSFSYKSSL", "down_seq": "CHHRCHTGEKPYKCNECGKS", "snv": [ { "evidence": [ { "id": "Q96N58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1906", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "52511373", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "T331", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "584", "end_pos": "584" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q96N58-1.311.311", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96N58-1.362.362", "start_pos": 362, "end_pos": 362, "uniprot_canonical_ac": "Q96N58-1", "length": 590, "uniprot_id": "ZN578_HUMAN", "protein_name": "Zinc finger protein 578", "refseq_ac": "NP_001093164", "refseq_name": "zinc finger protein 578", "gene_name": "ZNF578", "gene_names_uniprotkb": "ZNF578", "gene_names_refseq": "ZNF578", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96N58", "url": "https://www.uniprot.org/uniprotkb/Q96N58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96N58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PYKCNECGKSFSYKSSLRCH", "down_seq": "RLHTGIKPYKCNECGKMFGQ", "snv": [ { "evidence": [ { "id": "Q96N58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "52511465", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R362", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "584", "end_pos": "584" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96N58-1.454.454", "start_pos": 454, "end_pos": 454, "uniprot_canonical_ac": "Q96N58-1", "length": 590, "uniprot_id": "ZN578_HUMAN", "protein_name": "Zinc finger protein 578", "refseq_ac": "NP_001093164", "refseq_name": "zinc finger protein 578", "gene_name": "ZNF578", "gene_names_uniprotkb": "ZNF578", "gene_names_refseq": "ZNF578", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96N58", "url": "https://www.uniprot.org/uniprotkb/Q96N58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96N58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KAFIHQSSLARHHRLHTGEK", "down_seq": "YKCEECDRVFSQKSNLERHK", "snv": [ { "evidence": [ { "id": "Q96N58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "19", "chr_pos": "52511741", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S454", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." }, "synonyms": [ { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "tumor of the Ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "A primary or metastatic malignant neoplasm involving the ovary. Most primary malignant ovarian neoplasms are either carcinomas (serous, mucinous, or endometrioid adenocarcinomas) or malignant germ cell tumors. Metastatic malignant neoplasms to the ovary include carcinomas, lymphomas, and melanomas." }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "584", "end_pos": "584" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96N58-1.502.502", "start_pos": 502, "end_pos": 502, "uniprot_canonical_ac": "Q96N58-1", "length": 590, "uniprot_id": "ZN578_HUMAN", "protein_name": "Zinc finger protein 578", "refseq_ac": "NP_001093164", "refseq_name": "zinc finger protein 578", "gene_name": "ZNF578", "gene_names_uniprotkb": "ZNF578", "gene_names_refseq": "ZNF578", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96N58", "url": "https://www.uniprot.org/uniprotkb/Q96N58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96N58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PYKCNECHKTFSHRSSLPCH", "down_seq": "RLHSGEKPYKCNECGKTFNV", "snv": [ { "evidence": [ { "id": "Q96N58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "52511885", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R502", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "584", "end_pos": "584" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96N58-1.584.584", "start_pos": 584, "end_pos": 584, "uniprot_canonical_ac": "Q96N58-1", "length": 590, "uniprot_id": "ZN578_HUMAN", "protein_name": "Zinc finger protein 578", "refseq_ac": "NP_001093164", "refseq_name": "zinc finger protein 578", "gene_name": "ZNF578", "gene_names_uniprotkb": "ZNF578", "gene_names_refseq": "ZNF578", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96N58", "url": "https://www.uniprot.org/uniprotkb/Q96N58" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96N58", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "EKPYKCNECGKAHNHLIDSS", "down_seq": "KPCMSS", "snv": [ { "evidence": [ { "id": "Q96N58", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96N58" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "I", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "19", "chr_pos": "52512131", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "I584", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "211", "end_pos": "211" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "584", "end_pos": "584" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P39210-1.80.80", "start_pos": 80, "end_pos": 80, "uniprot_canonical_ac": "P39210-1", "length": 176, "uniprot_id": "MPV17_HUMAN", "protein_name": "Mitochondrial inner membrane protein Mpv17", "refseq_ac": "NP_002428", "refseq_name": "mitochondrial inner membrane protein Mpv17 isoform 3", "gene_name": "MPV17", "gene_names_uniprotkb": "MPV17", "gene_names_refseq": "CMT2EE; MPV17; MTDPS6; SYM1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P39210", "url": "https://www.uniprot.org/uniprotkb/P39210" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The Human Mitochondrial DNA Depletion Syndrome Gene MPV17 Encodes a Non-selective Channel That Modulates Membrane Potential.", "journal": "The Journal of biological chemistry", "date": "2015", "authors": "Antonenkov VD, Isomursu A, Mennerich D, Vapola MH, Weiher H, Kietzmann T, Hiltunen JK", "evidence": [ { "database": "UniProtKB", "id": "P39210", "url": "https://www.uniprot.org/uniprotkb/P39210" } ], "reference": [ { "type": "PubMed", "id": "25861990", "url": "https://glygen.org/publication/PubMed/25861990" } ] } ], "crossref": [ { "id": "P39210", "url": "https://www.uniprot.org/uniprotkb/P39210", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "25861990", "url": "https://glygen.org/publication/PubMed/25861990", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GFVGPVVGGWYKVLDRFIPG", "down_seq": "TKVDALKKMLLDQGGFAPCF", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "A", "comment": "Does not affect gating properties of the channel.", "evidence": [ { "database": "UniProtKB", "id": "P39210", "url": "https://www.uniprot.org/uniprotkb/P39210" }, { "database": "PubMed", "id": "25861990", "url": "https://glygen.org/publication/PubMed/25861990" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "80", "end_pos": "80" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "snv", "site_list": [ { "start_pos": "157", "end_pos": "157" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "P39210-1.92.92", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P39210-1.99.99", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39210-1.92.92", "start_pos": 92, "end_pos": 92, "uniprot_canonical_ac": "P39210-1", "length": 176, "uniprot_id": "MPV17_HUMAN", "protein_name": "Mitochondrial inner membrane protein Mpv17", "refseq_ac": "NP_002428", "refseq_name": "mitochondrial inner membrane protein Mpv17 isoform 3", "gene_name": "MPV17", "gene_names_uniprotkb": "MPV17", "gene_names_refseq": "CMT2EE; MPV17; MTDPS6; SYM1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P39210", "url": "https://www.uniprot.org/uniprotkb/P39210" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The Human Mitochondrial DNA Depletion Syndrome Gene MPV17 Encodes a Non-selective Channel That Modulates Membrane Potential.", "journal": "The Journal of biological chemistry", "date": "2015", "authors": "Antonenkov VD, Isomursu A, Mennerich D, Vapola MH, Weiher H, Kietzmann T, Hiltunen JK", "evidence": [ { "database": "UniProtKB", "id": "P39210", "url": "https://www.uniprot.org/uniprotkb/P39210" } ], "reference": [ { "type": "PubMed", "id": "25861990", "url": "https://glygen.org/publication/PubMed/25861990" } ] } ], "crossref": [ { "id": "P39210", "url": "https://www.uniprot.org/uniprotkb/P39210", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "25861990", "url": "https://glygen.org/publication/PubMed/25861990", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VLDRFIPGTTKVDALKKMLL", "down_seq": "QGGFAPCFLGCFLPLVGALN", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "K", "comment": "Affects ion selectivity of the channel.", "evidence": [ { "database": "UniProtKB", "id": "P39210", "url": "https://www.uniprot.org/uniprotkb/P39210" }, { "database": "PubMed", "id": "25861990", "url": "https://glygen.org/publication/PubMed/25861990" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "80", "end_pos": "80" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "snv", "site_list": [ { "start_pos": "157", "end_pos": "157" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P39210-1.80.80", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P39210-1.99.99", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39210-1.99.99", "start_pos": 99, "end_pos": 99, "uniprot_canonical_ac": "P39210-1", "length": 176, "uniprot_id": "MPV17_HUMAN", "protein_name": "Mitochondrial inner membrane protein Mpv17", "refseq_ac": "NP_002428", "refseq_name": "mitochondrial inner membrane protein Mpv17 isoform 3", "gene_name": "MPV17", "gene_names_uniprotkb": "MPV17", "gene_names_refseq": "CMT2EE; MPV17; MTDPS6; SYM1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P39210", "url": "https://www.uniprot.org/uniprotkb/P39210" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The Human Mitochondrial DNA Depletion Syndrome Gene MPV17 Encodes a Non-selective Channel That Modulates Membrane Potential.", "journal": "The Journal of biological chemistry", "date": "2015", "authors": "Antonenkov VD, Isomursu A, Mennerich D, Vapola MH, Weiher H, Kietzmann T, Hiltunen JK", "evidence": [ { "database": "UniProtKB", "id": "P39210", "url": "https://www.uniprot.org/uniprotkb/P39210" } ], "reference": [ { "type": "PubMed", "id": "25861990", "url": "https://glygen.org/publication/PubMed/25861990" } ] } ], "crossref": [ { "id": "P39210", "url": "https://www.uniprot.org/uniprotkb/P39210", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "25861990", "url": "https://glygen.org/publication/PubMed/25861990", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "GTTKVDALKKMLLDQGGFAP", "down_seq": "FLGCFLPLVGALNGLSAQDN", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "A", "comment": "Does not affect conductance and gating properties of the channel.", "evidence": [ { "database": "UniProtKB", "id": "P39210", "url": "https://www.uniprot.org/uniprotkb/P39210" }, { "database": "PubMed", "id": "25861990", "url": "https://glygen.org/publication/PubMed/25861990" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "80", "end_pos": "80" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "snv", "site_list": [ { "start_pos": "157", "end_pos": "157" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P39210-1.80.80", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P39210-1.92.92", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P39210-1.157.157", "start_pos": 157, "end_pos": 157, "uniprot_canonical_ac": "P39210-1", "length": 176, "uniprot_id": "MPV17_HUMAN", "protein_name": "Mitochondrial inner membrane protein Mpv17", "refseq_ac": "NP_002428", "refseq_name": "mitochondrial inner membrane protein Mpv17 isoform 3", "gene_name": "MPV17", "gene_names_uniprotkb": "MPV17", "gene_names_refseq": "CMT2EE; MPV17; MTDPS6; SYM1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P39210", "url": "https://www.uniprot.org/uniprotkb/P39210" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P39210", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P39210", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LWPAVQLANFYLVPLHYRLA", "down_seq": "VQCVAVIWNSYLSWKAHRL", "snv": [ { "evidence": [ { "id": "P39210", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P39210" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "27309974", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V157", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "80", "end_pos": "80" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "snv", "site_list": [ { "start_pos": "157", "end_pos": "157" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P39210-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "P39210-1", "length": 176, "uniprot_id": "MPV17_HUMAN", "protein_name": "Mitochondrial inner membrane protein Mpv17", "refseq_ac": "NP_002428", "refseq_name": "mitochondrial inner membrane protein Mpv17 isoform 3", "gene_name": "MPV17", "gene_names_uniprotkb": "MPV17", "gene_names_refseq": "CMT2EE; MPV17; MTDPS6; SYM1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P39210", "url": "https://www.uniprot.org/uniprotkb/P39210" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P39210", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P39210", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LTAGSLMGLGDIISQQLVER", "down_seq": "GLQEHQRGRTLTMVSLGCGF", "snv": [ { "evidence": [ { "id": "P39210", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P39210" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "2", "chr_pos": "27313058", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R41", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "80", "end_pos": "80" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "snv", "site_list": [ { "start_pos": "157", "end_pos": "157" }, { "start_pos": "41", "end_pos": "41" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEM7-1.482.482", "start_pos": 482, "end_pos": 482, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RPPPIKLPSSSGNSSSGNYF", "down_seq": "PQQTSSFLKSPTPPPSSKPS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr482", "evidence": [ { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "id": "Q8NEM7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q8NEM7-1.492.492", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8NEM7-1.494.494", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8NEM7-1.497.497", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8NEM7-1.498.498", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NEM7-1.499.499", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8NEM7-1.502.502", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 13 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NEM7-1.492.492", "start_pos": 492, "end_pos": 492, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SGNSSSGNYFTPQQTSSFLK", "down_seq": "PTPPPSSKPSSIPRKSSVDL", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser492", "evidence": [ { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "id": "Q8NEM7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "Q8NEM7", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8NEM7-1.482.482", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NEM7-1.494.494", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NEM7-1.497.497", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8NEM7-1.498.498", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8NEM7-1.499.499", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8NEM7-1.502.502", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8NEM7-1.503.503", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8NEM7-1.508.508", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 13 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NEM7-1.494.494", "start_pos": 494, "end_pos": 494, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" }, { "database": "iPTMnet", "id": "Q8NEM7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs751312421", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751312421", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751312421", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751312421", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751312421", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751312421#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs751312421", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751312421", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NSSSGNYFTPQQTSSFLKSP", "down_seq": "PPPSSKPSSIPRKSSVDLNQ", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr494", "evidence": [ { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "id": "Q8NEM7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "Q8NEM7", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ] }, { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr494", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs751312421", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751312421" }, { "id": "rs751312421", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751312421" }, { "id": "rs751312421", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751312421#frequency_tab" }, { "id": "rs751312421", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751312421" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->P).", "chr_id": "13", "chr_pos": "37024146", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T494", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q8NEM7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7" } ], "site_lbl": "Thr494" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8NEM7-1.482.482", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NEM7-1.492.492", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NEM7-1.497.497", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8NEM7-1.498.498", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NEM7-1.499.499", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8NEM7-1.502.502", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8NEM7-1.503.503", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8NEM7-1.508.508", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 14 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NEM7-1.498.498", "start_pos": 498, "end_pos": 498, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs143941016", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143941016", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs143941016", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143941016#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs143941016", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143941016", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GNYFTPQQTSSFLKSPTPPP", "down_seq": "SKPSSIPRKSSVDLNQVSML", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser498", "evidence": [ { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "id": "Q8NEM7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "Q8NEM7", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ] } ], "snv": [ { "evidence": [ { "id": "rs143941016", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143941016" }, { "id": "rs143941016", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143941016#frequency_tab" }, { "id": "rs143941016", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143941016" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->P).", "chr_id": "13", "chr_pos": "37024134", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S498", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8NEM7-1.482.482", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8NEM7-1.492.492", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8NEM7-1.494.494", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NEM7-1.497.497", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NEM7-1.499.499", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8NEM7-1.502.502", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NEM7-1.503.503", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8NEM7-1.508.508", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8NEM7-1.516.516", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 13 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NEM7-1.499.499", "start_pos": 499, "end_pos": 499, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Methods for Enrichment and Assignment of N-Acetylglucosamine Modification Sites.", "journal": "Molecular & cellular proteomics : MCP", "date": "2021", "authors": "Maynard JC, Chalkley RJ", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750" } ] } ], "crossref": [ { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "rs752386919", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752386919", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752386919", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752386919", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752386919", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752386919#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs752386919", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752386919", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NYFTPQQTSSFLKSPTPPPS", "down_seq": "KPSSIPRKSSVDLNQVSMLS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser499", "evidence": [ { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "id": "Q8NEM7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "Q8NEM7", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" }, { "id": "32938750", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32938750" } ] }, { "glytoucan_ac": "G70994MS", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser499", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "GLY_000142", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000142" } ] } ], "snv": [ { "evidence": [ { "id": "rs752386919", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752386919" }, { "id": "rs752386919", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752386919" }, { "id": "rs752386919", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752386919#frequency_tab" }, { "id": "rs752386919", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752386919" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->C).", "chr_id": "13", "chr_pos": "37024130", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S499", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8NEM7-1.482.482", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8NEM7-1.492.492", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8NEM7-1.494.494", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8NEM7-1.497.497", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NEM7-1.498.498", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NEM7-1.502.502", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8NEM7-1.503.503", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8NEM7-1.508.508", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NEM7-1.516.516", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8NEM7-1.519.519", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 2 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 2 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 14 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NEM7-1.502.502", "start_pos": 502, "end_pos": 502, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TPQQTSSFLKSPTPPPSSKP", "down_seq": "SIPRKSSVDLNQVSMLSPAA", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser502", "evidence": [ { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "id": "Q8NEM7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "Q8NEM7", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8NEM7-1.482.482", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8NEM7-1.492.492", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8NEM7-1.494.494", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8NEM7-1.497.497", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8NEM7-1.498.498", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NEM7-1.499.499", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NEM7-1.503.503", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8NEM7-1.508.508", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8NEM7-1.516.516", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8NEM7-1.519.519", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 13 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NEM7-1.503.503", "start_pos": 503, "end_pos": 503, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q8NEM7-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs201078985", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201078985", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201078985", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201078985", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201078985", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201078985", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201078985", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201078985#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201078985", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201078985", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2061804464", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2061804464", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2061804464", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2061804464#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2061804464", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2061804464", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PQQTSSFLKSPTPPPSSKPS", "down_seq": "IPRKSSVDLNQVSMLSPAAL", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser503", "evidence": [ { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "id": "Q8NEM7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "Q8NEM7", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ] } ], "snv": [ { "evidence": [ { "id": "rs201078985", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201078985" }, { "id": "rs201078985", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201078985" }, { "id": "rs201078985", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201078985" }, { "id": "rs201078985", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201078985#frequency_tab" }, { "id": "rs201078985", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201078985" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->G).", "chr_id": "13", "chr_pos": "37024119", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "S503", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2061804464", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2061804464" }, { "id": "rs2061804464", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2061804464#frequency_tab" }, { "id": "rs2061804464", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2061804464" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->N).", "chr_id": "13", "chr_pos": "37024118", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S503", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs201078985", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201078985" }, { "id": "rs201078985", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201078985" }, { "id": "rs201078985", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201078985" }, { "id": "rs201078985", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201078985#frequency_tab" }, { "id": "rs201078985", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201078985" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->R).", "chr_id": "13", "chr_pos": "37024119", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "S503", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NEM7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser503" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8NEM7-1.492.492", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8NEM7-1.494.494", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8NEM7-1.497.497", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8NEM7-1.498.498", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8NEM7-1.499.499", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NEM7-1.502.502", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NEM7-1.508.508", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8NEM7-1.516.516", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8NEM7-1.519.519", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 14 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NEM7-1.516.516", "start_pos": 516, "end_pos": 516, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "database": "O-GlcNAc Atlas", "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "https://oglcnac.org/atlas/detail/Q8NEM7", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PPSSKPSSIPRKSSVDLNQV", "down_seq": "MLSPAALSPASSSQRTTATQ", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser516", "evidence": [ { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "id": "Q8NEM7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NEM7" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "31492838", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31492838" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "35132862", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35132862" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "Q8NEM7", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8NEM7" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8NEM7-1.497.497", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8NEM7-1.498.498", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8NEM7-1.499.499", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8NEM7-1.502.502", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8NEM7-1.503.503", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8NEM7-1.508.508", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NEM7-1.519.519", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8NEM7-1.524.524", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 13 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NEM7-1.575.575", "start_pos": 575, "end_pos": 575, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GAQALMSGSNPMLGCNTGAI", "down_seq": "PAGINLSGLLPSGGLLPNAL", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr575", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEM7-1.20.20", "start_pos": 20, "end_pos": 20, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NEM7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEM7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "", "down_seq": "QRPPKRKYLSSGRKSVFQKL", "snv": [ { "evidence": [ { "id": "Q8NEM7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEM7" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "13", "chr_pos": "37047918", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R20", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEM7-1.216.216", "start_pos": 216, "end_pos": 216, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757682924", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757682924", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757682924", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757682924", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757682924", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757682924", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ESQLILATAEPLCLDPSIAV", "down_seq": "CTANRLLYNKQKMNTRPMKR", "snv": [ { "evidence": [ { "id": "rs757682924", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757682924" }, { "id": "rs757682924", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757682924" }, { "id": "rs757682924", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757682924" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TCT->NCT).", "chr_id": "13", "chr_pos": "37033509", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T216", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q8NEM7-1.232.232", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEM7-1.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NEM7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEM7", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs569498102", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs569498102", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs569498102", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs569498102", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs569498102", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs569498102", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs569498102", "url": "https://www.ncbi.nlm.nih.gov/snp/rs569498102#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs569498102", "url": "http://gnomad.broadinstitute.org/awesome?query=rs569498102", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs569498102", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs569498102", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SIAVTCTANRLLYNKQKMNT", "down_seq": "PMKRCFKRYSRSSLNRQQDL", "snv": [ { "evidence": [ { "id": "Q8NEM7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEM7" }, { "id": "rs569498102", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs569498102" }, { "id": "rs569498102", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs569498102" }, { "id": "rs569498102", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs569498102" }, { "id": "rs569498102", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs569498102#frequency_tab" }, { "id": "rs569498102", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs569498102" }, { "id": "rs569498102", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs569498102" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NTR->NTC).", "chr_id": "13", "chr_pos": "37033462", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R232", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8NEM7-1.216.216", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEM7-1.321.321", "start_pos": 321, "end_pos": 321, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NEM7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEM7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AIPSEVDVEKYAKVEKSIKS", "down_seq": "DSQPTVWPAHDVKDDYVFEC", "snv": [ { "evidence": [ { "id": "Q8NEM7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEM7" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DDS->NDS).", "chr_id": "13", "chr_pos": "37029797", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D321", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEM7-1.376.376", "start_pos": 376, "end_pos": 376, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1010295214", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1010295214", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1010295214", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1010295214#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1010295214", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1010295214", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QSLGDPLYYGKIQPCKADEE", "down_seq": "DSQMSPSHSSTDDHSNWFII", "snv": [ { "evidence": [ { "id": "rs1010295214", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1010295214" }, { "id": "rs1010295214", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1010295214#frequency_tab" }, { "id": "rs1010295214", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1010295214" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SDS->NDS).", "chr_id": "13", "chr_pos": "37028172", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S376", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q8NEM7-1.381.381", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEM7-1.409.409", "start_pos": 409, "end_pos": 409, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NEM7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEM7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DHSNWFIIGSKTDAERVVNQ", "down_seq": "QELVQNEAKCPVKMSHSSSG", "snv": [ { "evidence": [ { "id": "Q8NEM7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEM7" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Y", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NQY->NQC).", "chr_id": "13", "chr_pos": "37025423", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "Y409", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q8NEM7-1.417.417", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEM7-1.417.417", "start_pos": 417, "end_pos": 417, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2062075416", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2062075416", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2062075416", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2062075416#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GSKTDAERVVNQYQELVQNE", "down_seq": "KCPVKMSHSSSGSASLSQVS", "snv": [ { "evidence": [ { "id": "rs2062075416", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2062075416" }, { "id": "rs2062075416", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2062075416#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEA->NET).", "chr_id": "13", "chr_pos": "37025400", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A417", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8NEM7-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8NEM7-1.437.437", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEM7-1.497.497", "start_pos": 497, "end_pos": 497, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NEM7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEM7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "SGNYFTPQQTSSFLKSPTPP", "down_seq": "SSKPSSIPRKSSVDLNQVSM", "snv": [ { "evidence": [ { "id": "Q8NEM7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEM7" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "13", "chr_pos": "37024137", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P497", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8NEM7-1.482.482", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8NEM7-1.492.492", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NEM7-1.494.494", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NEM7-1.498.498", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8NEM7-1.499.499", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NEM7-1.502.502", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8NEM7-1.503.503", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8NEM7-1.508.508", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8NEM7-1.516.516", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEM7-1.547.547", "start_pos": 547, "end_pos": 547, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs772081986", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772081986", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772081986", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772081986", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772081986", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772081986", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "SSSQRTTATQVMANSAGLNF", "down_seq": "NVVGSVCGAQALMSGSNPML", "snv": [ { "evidence": [ { "id": "rs772081986", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772081986" }, { "id": "rs772081986", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772081986" }, { "id": "rs772081986", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772081986" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFI->NFT).", "chr_id": "13", "chr_pos": "37022032", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I547", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEM7-1.763.763", "start_pos": 763, "end_pos": 763, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NEM7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEM7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MAMAAAAAQTAQLHHHRHTG", "down_seq": "QSKSKMKRGTPTTPKF", "snv": [ { "evidence": [ { "id": "Q8NEM7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEM7" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SQS->NQS).", "chr_id": "13", "chr_pos": "37009724", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S763", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q8NEM7-1.779.779", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEM7-1.779.779", "start_pos": 779, "end_pos": 779, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NEM7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEM7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "RHTGSQSKSKMKRGTPTTPK", "down_seq": "", "snv": [ { "evidence": [ { "id": "Q8NEM7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NEM7" } ], "glycoeffect": [], "subjects_tested": "606", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "F", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "13", "chr_pos": "37009676", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "F779", "disease": [ { "disease_id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid cancer", "description": "An endocrine gland cancer located in the thyroid gland located in the neck below the thyroid cartilage." }, "synonyms": [ { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "Thyroid gland neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant tumour of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid gland cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3973", "DOID:0080524", "DOID:0080525" ], "evidence": [ { "id": "1781", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1781" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8NEM7-1.763.763", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEM7-1.81.81", "start_pos": 81, "end_pos": 81, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1316115049", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1316115049", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1316115049", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1316115049#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1316115049", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1316115049", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VNLLEKLVMQETLSCLVVNL", "down_seq": "PGNEGYSLMLRGKNGSDSET", "snv": [ { "evidence": [ { "id": "rs1316115049", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1316115049" }, { "id": "rs1316115049", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1316115049#frequency_tab" }, { "id": "rs1316115049", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1316115049" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLY->NLC).", "chr_id": "13", "chr_pos": "37045297", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y81", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEM7-1.296.296", "start_pos": 296, "end_pos": 296, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GQHYDLKISKAGNCVDMWKR", "down_seq": "PCNLAIPSEVDVEKYAKVEK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "site_lbl": "Ser296" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NEM7-1.381.381", "start_pos": 381, "end_pos": 381, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Motif-specific sampling of phosphoproteomes.", "journal": "Journal of proteome research", "date": "2008", "authors": "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "evidence": [ { "database": "iPTMnet", "id": "Q8NEM7-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "Q8NEM7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PLYYGKIQPCKADEESDSQM", "down_seq": "PSHSSTDDHSNWFIIGSKTD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NEM7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser381" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q8NEM7-1.376.376", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NEM7-1.437.437", "start_pos": 437, "end_pos": 437, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Motif-specific sampling of phosphoproteomes.", "journal": "Journal of proteome research", "date": "2008", "authors": "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "evidence": [ { "database": "iPTMnet", "id": "Q8NEM7-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Pan C, Olsen JV, Daub H, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q8NEM7-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q8NEM7-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8NEM7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AKCPVKMSHSSSGSASLSQV", "down_seq": "PGKETDQTETVSVQSSVLGK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NEM7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser437" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8NEM7-1.417.417", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NEM7-1.508.508", "start_pos": 508, "end_pos": 508, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q8NEM7-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8NEM7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SFLKSPTPPPSSKPSSIPRK", "down_seq": "SVDLNQVSMLSPAALSPASS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8NEM7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser508" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8NEM7-1.492.492", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8NEM7-1.494.494", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8NEM7-1.497.497", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8NEM7-1.498.498", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8NEM7-1.499.499", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8NEM7-1.502.502", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8NEM7-1.503.503", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8NEM7-1.516.516", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8NEM7-1.519.519", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8NEM7-1.524.524", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NEM7-1.519.519", "start_pos": 519, "end_pos": 519, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.", "journal": "Science signaling", "date": "2009", "authors": "Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK", "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" }, { "database": "iPTMnet", "id": "Q8NEM7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] } ], "crossref": [ { "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NEM7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SKPSSIPRKSSVDLNQVSML", "down_seq": "PAALSPASSSQRTTATQVMA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "iPTMnet", "id": "Q8NEM7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7" } ], "site_lbl": "Ser519" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8NEM7-1.499.499", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8NEM7-1.502.502", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8NEM7-1.503.503", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8NEM7-1.508.508", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NEM7-1.516.516", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NEM7-1.524.524", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NEM7-1.524.524", "start_pos": 524, "end_pos": 524, "uniprot_canonical_ac": "Q8NEM7-1", "length": 779, "uniprot_id": "SP20H_HUMAN", "protein_name": "Transcription factor SPT20 homolog", "refseq_ac": "NP_001014308", "refseq_name": "transcription factor SPT20 homolog isoform a", "gene_name": "SUPT20H", "gene_names_uniprotkb": "SUPT20H; C13orf19; FAM48A; FP757", "gene_names_refseq": "C13orf19; C13; FAM48A; FP757; P38IP; SPT20; SUPT20H", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q8NEM7-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q8NEM7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IPRKSSVDLNQVSMLSPAAL", "down_seq": "PASSSQRTTATQVMANSAGL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NEM7", "url": "https://www.uniprot.org/uniprotkb/Q8NEM7" }, { "database": "iPTMnet", "id": "Q8NEM7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NEM7" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser524" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "482", "end_pos": "482" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "575", "end_pos": "575" } ] }, { "type": "snv", "site_list": [ { "start_pos": "20", "end_pos": "20" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "499", "end_pos": "499" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "763", "end_pos": "763" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "81", "end_pos": "81" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "296", "end_pos": "296" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "524", "end_pos": "524" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8NEM7-1.508.508", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8NEM7-1.516.516", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8NEM7-1.519.519", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BUB5-1.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "Q9BUB5-1", "length": 465, "uniprot_id": "MKNK1_HUMAN", "protein_name": "MAP kinase-interacting serine/threonine-protein kinase 1", "refseq_ac": "NP_945324", "refseq_name": "MAP kinase-interacting serine/threonine-protein kinase 1 isoform 2", "gene_name": "MKNK1", "gene_names_uniprotkb": "MKNK1; MNK1", "gene_names_refseq": "MKNK1; MNK1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Negative regulation of protein translation by mitogen-activated protein kinase-interacting kinases 1 and 2.", "journal": "Molecular and cellular biology", "date": "2001", "authors": "Knauf U, Tschopp C, Gram H", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832" } ] } ], "crossref": [ { "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LKPENILCESPEKVSPVKIC", "down_seq": "FDLGSGMKLNNSCTPITTPE", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Loss of kinase activity; when associated with K-78.", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "PubMed", "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "snv", "site_list": [ { "start_pos": "308", "end_pos": "308" }, { "start_pos": "402", "end_pos": "402" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "191", "end_pos": "191" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "460", "end_pos": "460" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9BUB5-1.221.221", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9BUB5-1.226.226", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9BUB5-1.250.250", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BUB5-1.250.250", "start_pos": 250, "end_pos": 250, "uniprot_canonical_ac": "Q9BUB5-1", "length": 465, "uniprot_id": "MKNK1_HUMAN", "protein_name": "MAP kinase-interacting serine/threonine-protein kinase 1", "refseq_ac": "NP_945324", "refseq_name": "MAP kinase-interacting serine/threonine-protein kinase 1 isoform 2", "gene_name": "MKNK1", "gene_names_uniprotkb": "MKNK1; MNK1", "gene_names_refseq": "MKNK1; MNK1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Negative regulation of protein translation by mitogen-activated protein kinase-interacting kinases 1 and 2.", "journal": "Molecular and cellular biology", "date": "2001", "authors": "Knauf U, Tschopp C, Gram H", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832" } ] }, { "title": "Characterization of the activity of human MAP kinase-interacting kinase Mnk1b.", "journal": "Biochimica et biophysica acta", "date": "2007", "authors": "O'Loghlen A, Gonzalez VM, Jurado T, Salinas M, Martin ME", "evidence": [ { "database": "RefSeq", "id": "NP_945324", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_945324" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "17590453", "url": "https://glygen.org/publication/PubMed/17590453" } ] }, { "title": "Mitogen-activated protein kinases activate the serine/threonine kinases Mnk1 and Mnk2.", "journal": "The EMBO journal", "date": "1997", "authors": "Waskiewicz AJ, Flynn A, Proud CG, Cooper JA", "evidence": [ { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "9155017", "url": "https://glygen.org/publication/PubMed/9155017" } ] }, { "title": "The mitogen-activated protein kinase signal-integrating kinase Mnk2 is a eukaryotic initiation factor 4E kinase with high levels of basal activity in mammalian cells.", "journal": "Molecular and cellular biology", "date": "2001", "authors": "Scheper GC, Morrice NA, Kleijn M, Proud CG", "evidence": [ { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "11154262", "url": "https://glygen.org/publication/PubMed/11154262" } ] }, { "title": "Identification and molecular characterization of Mnk1b, a splice variant of human MAP kinase-interacting kinase Mnk1.", "journal": "Experimental cell research", "date": "2004", "authors": "O'Loghlen A, Gonzalez VM, Pineiro D, Perez-Morgado MI, Salinas M, Martin ME", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "15350534", "url": "https://glygen.org/publication/PubMed/15350534" } ] }, { "title": "Protein phosphatase 2A negatively regulates eukaryotic initiation factor 4E phosphorylation and eIF4F assembly through direct dephosphorylation of Mnk and eIF4E.", "journal": "Neoplasia (New York, N.Y.)", "date": "2010", "authors": "Li Y, Yue P, Deng X, Ueda T, Fukunaga R, Khuri FR, Sun SY", "evidence": [ { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "20927323", "url": "https://glygen.org/publication/PubMed/20927323" } ] } ], "crossref": [ { "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17590453", "url": "https://glygen.org/publication/PubMed/17590453", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9155017", "url": "https://glygen.org/publication/PubMed/9155017", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11154262", "url": "https://glygen.org/publication/PubMed/11154262", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15350534", "url": "https://glygen.org/publication/PubMed/15350534", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BUB5", "url": "https://www.ebi.ac.uk/intact/interactors/id:Q9BUB5*", "database": "IntAct", "categories": [ "Other" ] }, { "id": "20927323", "url": "https://glygen.org/publication/PubMed/20927323", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BUB5", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q9BUB5", "database": "PRO", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ICDFDLGSGMKLNNSCTPIT", "down_seq": "PELTTPCGSAEYMAPEVVEV", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "A", "comment": "Loss of kinase activity; when associated with T-255.", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "PubMed", "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q16539-1", "kinase_gene_name": "MAPK14", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" }, { "database": "PubMed", "id": "17590453", "url": "https://glygen.org/publication/PubMed/17590453" }, { "database": "PubMed", "id": "9155017", "url": "https://glygen.org/publication/PubMed/9155017" } ], "site_lbl": "Thr250" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "PubMed", "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" }, { "database": "PubMed", "id": "11154262", "url": "https://glygen.org/publication/PubMed/11154262" }, { "database": "PubMed", "id": "15350534", "url": "https://glygen.org/publication/PubMed/15350534" }, { "database": "IntAct", "id": "Q9BUB5", "url": "https://www.ebi.ac.uk/intact/interactors/id:Q9BUB5*" }, { "database": "PubMed", "id": "20927323", "url": "https://glygen.org/publication/PubMed/20927323" }, { "database": "PRO", "id": "Q9BUB5", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q9BUB5" } ], "site_lbl": "Thr250" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "snv", "site_list": [ { "start_pos": "308", "end_pos": "308" }, { "start_pos": "402", "end_pos": "402" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "191", "end_pos": "191" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "460", "end_pos": "460" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9BUB5-1.232.232", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9BUB5-1.255.255", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BUB5-1.255.255", "start_pos": 255, "end_pos": 255, "uniprot_canonical_ac": "Q9BUB5-1", "length": 465, "uniprot_id": "MKNK1_HUMAN", "protein_name": "MAP kinase-interacting serine/threonine-protein kinase 1", "refseq_ac": "NP_945324", "refseq_name": "MAP kinase-interacting serine/threonine-protein kinase 1 isoform 2", "gene_name": "MKNK1", "gene_names_uniprotkb": "MKNK1; MNK1", "gene_names_refseq": "MKNK1; MNK1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Negative regulation of protein translation by mitogen-activated protein kinase-interacting kinases 1 and 2.", "journal": "Molecular and cellular biology", "date": "2001", "authors": "Knauf U, Tschopp C, Gram H", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832" } ] }, { "title": "Characterization of the activity of human MAP kinase-interacting kinase Mnk1b.", "journal": "Biochimica et biophysica acta", "date": "2007", "authors": "O'Loghlen A, Gonzalez VM, Jurado T, Salinas M, Martin ME", "evidence": [ { "database": "RefSeq", "id": "NP_945324", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_945324" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "17590453", "url": "https://glygen.org/publication/PubMed/17590453" } ] }, { "title": "Mitogen-activated protein kinases activate the serine/threonine kinases Mnk1 and Mnk2.", "journal": "The EMBO journal", "date": "1997", "authors": "Waskiewicz AJ, Flynn A, Proud CG, Cooper JA", "evidence": [ { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "9155017", "url": "https://glygen.org/publication/PubMed/9155017" } ] }, { "title": "The mitogen-activated protein kinase signal-integrating kinase Mnk2 is a eukaryotic initiation factor 4E kinase with high levels of basal activity in mammalian cells.", "journal": "Molecular and cellular biology", "date": "2001", "authors": "Scheper GC, Morrice NA, Kleijn M, Proud CG", "evidence": [ { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "11154262", "url": "https://glygen.org/publication/PubMed/11154262" } ] }, { "title": "Identification and molecular characterization of Mnk1b, a splice variant of human MAP kinase-interacting kinase Mnk1.", "journal": "Experimental cell research", "date": "2004", "authors": "O'Loghlen A, Gonzalez VM, Pineiro D, Perez-Morgado MI, Salinas M, Martin ME", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "15350534", "url": "https://glygen.org/publication/PubMed/15350534" } ] }, { "title": "Protein phosphatase 2A negatively regulates eukaryotic initiation factor 4E phosphorylation and eIF4F assembly through direct dephosphorylation of Mnk and eIF4E.", "journal": "Neoplasia (New York, N.Y.)", "date": "2010", "authors": "Li Y, Yue P, Deng X, Ueda T, Fukunaga R, Khuri FR, Sun SY", "evidence": [ { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "20927323", "url": "https://glygen.org/publication/PubMed/20927323" } ] } ], "crossref": [ { "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17590453", "url": "https://glygen.org/publication/PubMed/17590453", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9155017", "url": "https://glygen.org/publication/PubMed/9155017", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11154262", "url": "https://glygen.org/publication/PubMed/11154262", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15350534", "url": "https://glygen.org/publication/PubMed/15350534", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BUB5", "url": "https://www.ebi.ac.uk/intact/interactors/id:Q9BUB5*", "database": "IntAct", "categories": [ "Other" ] }, { "id": "20927323", "url": "https://glygen.org/publication/PubMed/20927323", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BUB5", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q9BUB5", "database": "PRO", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LGSGMKLNNSCTPITTPELT", "down_seq": "PCGSAEYMAPEVVEVFTDQA", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "A", "comment": "Loss of kinase activity; when associated with T-250.", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "PubMed", "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q16539-1", "kinase_gene_name": "MAPK14", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" }, { "database": "PubMed", "id": "17590453", "url": "https://glygen.org/publication/PubMed/17590453" }, { "database": "PubMed", "id": "9155017", "url": "https://glygen.org/publication/PubMed/9155017" } ], "site_lbl": "Thr255" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "PubMed", "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" }, { "database": "PubMed", "id": "11154262", "url": "https://glygen.org/publication/PubMed/11154262" }, { "database": "PubMed", "id": "15350534", "url": "https://glygen.org/publication/PubMed/15350534" }, { "database": "IntAct", "id": "Q9BUB5", "url": "https://www.ebi.ac.uk/intact/interactors/id:Q9BUB5*" }, { "database": "PubMed", "id": "20927323", "url": "https://glygen.org/publication/PubMed/20927323" }, { "database": "PRO", "id": "Q9BUB5", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q9BUB5" } ], "site_lbl": "Thr255" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "snv", "site_list": [ { "start_pos": "308", "end_pos": "308" }, { "start_pos": "402", "end_pos": "402" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "191", "end_pos": "191" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "460", "end_pos": "460" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9BUB5-1.250.250", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BUB5-1.385.385", "start_pos": 385, "end_pos": 385, "uniprot_canonical_ac": "Q9BUB5-1", "length": 465, "uniprot_id": "MKNK1_HUMAN", "protein_name": "MAP kinase-interacting serine/threonine-protein kinase 1", "refseq_ac": "NP_945324", "refseq_name": "MAP kinase-interacting serine/threonine-protein kinase 1 isoform 2", "gene_name": "MKNK1", "gene_names_uniprotkb": "MKNK1; MNK1", "gene_names_refseq": "MKNK1; MNK1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Negative regulation of protein translation by mitogen-activated protein kinase-interacting kinases 1 and 2.", "journal": "Molecular and cellular biology", "date": "2001", "authors": "Knauf U, Tschopp C, Gram H", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832" } ] }, { "title": "MNK1, a new MAP kinase-activated protein kinase, isolated by a novel expression screening method for identifying protein kinase substrates.", "journal": "The EMBO journal", "date": "1997", "authors": "Fukunaga R, Hunter T", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "9155018", "url": "https://glygen.org/publication/PubMed/9155018" } ] }, { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "9155018", "url": "https://glygen.org/publication/PubMed/9155018", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BUB5", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q9BUB5", "database": "PRO", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AAQVLQHPWVQGQAPEKGLP", "down_seq": "PQVLQRNSSTMDLTLFAAEA", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "D", "comment": "Constitutively active.", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "PubMed", "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P27361-1", "kinase_gene_name": "MAPK3", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" }, { "database": "PubMed", "id": "9155018", "url": "https://glygen.org/publication/PubMed/9155018" } ], "site_lbl": "Thr385" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832" }, { "database": "PRO", "id": "Q9BUB5", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q9BUB5" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "site_lbl": "Thr385" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "snv", "site_list": [ { "start_pos": "308", "end_pos": "308" }, { "start_pos": "402", "end_pos": "402" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "191", "end_pos": "191" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "460", "end_pos": "460" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q9BUB5-1.402.402", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BUB5-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "Q9BUB5-1", "length": 465, "uniprot_id": "MKNK1_HUMAN", "protein_name": "MAP kinase-interacting serine/threonine-protein kinase 1", "refseq_ac": "NP_945324", "refseq_name": "MAP kinase-interacting serine/threonine-protein kinase 1 isoform 2", "gene_name": "MKNK1", "gene_names_uniprotkb": "MKNK1; MNK1", "gene_names_refseq": "MKNK1; MNK1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Negative regulation of protein translation by mitogen-activated protein kinase-interacting kinases 1 and 2.", "journal": "Molecular and cellular biology", "date": "2001", "authors": "Knauf U, Tschopp C, Gram H", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832" } ] } ], "crossref": [ { "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "GAYAKVQGAVSLQNGKEYAV", "down_seq": "IIEKQAGHSRSRVFREVETL", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "M", "comment": "Loss of kinase activity; when associated with D-232.", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "PubMed", "id": "11463832", "url": "https://glygen.org/publication/PubMed/11463832" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "snv", "site_list": [ { "start_pos": "308", "end_pos": "308" }, { "start_pos": "402", "end_pos": "402" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "191", "end_pos": "191" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "460", "end_pos": "460" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BUB5-1.308.308", "start_pos": 308, "end_pos": 308, "uniprot_canonical_ac": "Q9BUB5-1", "length": 465, "uniprot_id": "MKNK1_HUMAN", "protein_name": "MAP kinase-interacting serine/threonine-protein kinase 1", "refseq_ac": "NP_945324", "refseq_name": "MAP kinase-interacting serine/threonine-protein kinase 1 isoform 2", "gene_name": "MKNK1", "gene_names_uniprotkb": "MKNK1; MNK1", "gene_names_refseq": "MKNK1; MNK1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BUB5", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BUB5", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GVVLYIMLSGYPPFVGHCGA", "down_seq": "CGWDRGEVCRVCQNKLFESI", "snv": [ { "evidence": [ { "id": "Q9BUB5", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BUB5" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "1", "chr_pos": "46562690", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D308", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "snv", "site_list": [ { "start_pos": "308", "end_pos": "308" }, { "start_pos": "402", "end_pos": "402" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "191", "end_pos": "191" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "460", "end_pos": "460" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BUB5-1.402.402", "start_pos": 402, "end_pos": 402, "uniprot_canonical_ac": "Q9BUB5-1", "length": 465, "uniprot_id": "MKNK1_HUMAN", "protein_name": "MAP kinase-interacting serine/threonine-protein kinase 1", "refseq_ac": "NP_945324", "refseq_name": "MAP kinase-interacting serine/threonine-protein kinase 1 isoform 2", "gene_name": "MKNK1", "gene_names_uniprotkb": "MKNK1; MNK1", "gene_names_refseq": "MKNK1; MNK1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BUB5", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BUB5", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GLPTPQVLQRNSSTMDLTLF", "down_seq": "AEAIALNRQLSQHEENELAE", "snv": [ { "evidence": [ { "id": "Q9BUB5", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BUB5" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "46558769", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A402", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "snv", "site_list": [ { "start_pos": "308", "end_pos": "308" }, { "start_pos": "402", "end_pos": "402" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "191", "end_pos": "191" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "460", "end_pos": "460" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9BUB5-1.385.385", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BUB5-1.191.191", "start_pos": 191, "end_pos": 191, "uniprot_canonical_ac": "Q9BUB5-1", "length": 465, "uniprot_id": "MKNK1_HUMAN", "protein_name": "MAP kinase-interacting serine/threonine-protein kinase 1", "refseq_ac": "NP_945324", "refseq_name": "MAP kinase-interacting serine/threonine-protein kinase 1 isoform 2", "gene_name": "MKNK1", "gene_names_uniprotkb": "MKNK1; MNK1", "gene_names_refseq": "MKNK1; MNK1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Features of the catalytic domains and C termini of the MAPK signal-integrating kinases Mnk1 and Mnk2 determine their differing activities and regulatory properties.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Parra JL, Buxade M, Proud CG", "evidence": [ { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "16162500", "url": "https://glygen.org/publication/PubMed/16162500" } ] } ], "crossref": [ { "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "16162500", "url": "https://glygen.org/publication/PubMed/16162500", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HLGWSAMAPSGLTAAPTSLG", "down_seq": "SDPPTSASQVAGTTGIAHRD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" }, { "database": "PubMed", "id": "16162500", "url": "https://glygen.org/publication/PubMed/16162500" } ], "site_lbl": "Ser191" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "snv", "site_list": [ { "start_pos": "308", "end_pos": "308" }, { "start_pos": "402", "end_pos": "402" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "191", "end_pos": "191" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "460", "end_pos": "460" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BUB5-1.221.221", "start_pos": 221, "end_pos": 221, "uniprot_canonical_ac": "Q9BUB5-1", "length": 465, "uniprot_id": "MKNK1_HUMAN", "protein_name": "MAP kinase-interacting serine/threonine-protein kinase 1", "refseq_ac": "NP_945324", "refseq_name": "MAP kinase-interacting serine/threonine-protein kinase 1 isoform 2", "gene_name": "MKNK1", "gene_names_uniprotkb": "MKNK1; MNK1", "gene_names_refseq": "MKNK1; MNK1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VAGTTGIAHRDLKPENILCE", "down_seq": "PEKVSPVKICDFDLGSGMKL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "site_lbl": "Ser221" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "snv", "site_list": [ { "start_pos": "308", "end_pos": "308" }, { "start_pos": "402", "end_pos": "402" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "191", "end_pos": "191" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "460", "end_pos": "460" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q9BUB5-1.226.226", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9BUB5-1.232.232", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BUB5-1.226.226", "start_pos": 226, "end_pos": 226, "uniprot_canonical_ac": "Q9BUB5-1", "length": 465, "uniprot_id": "MKNK1_HUMAN", "protein_name": "MAP kinase-interacting serine/threonine-protein kinase 1", "refseq_ac": "NP_945324", "refseq_name": "MAP kinase-interacting serine/threonine-protein kinase 1 isoform 2", "gene_name": "MKNK1", "gene_names_uniprotkb": "MKNK1; MNK1", "gene_names_refseq": "MKNK1; MNK1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GIAHRDLKPENILCESPEKV", "down_seq": "PVKICDFDLGSGMKLNNSCT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "site_lbl": "Ser226" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "snv", "site_list": [ { "start_pos": "308", "end_pos": "308" }, { "start_pos": "402", "end_pos": "402" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "191", "end_pos": "191" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "460", "end_pos": "460" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9BUB5-1.221.221", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9BUB5-1.232.232", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BUB5-1.39.39", "start_pos": 39, "end_pos": 39, "uniprot_canonical_ac": "Q9BUB5-1", "length": 465, "uniprot_id": "MKNK1_HUMAN", "protein_name": "MAP kinase-interacting serine/threonine-protein kinase 1", "refseq_ac": "NP_945324", "refseq_name": "MAP kinase-interacting serine/threonine-protein kinase 1 isoform 2", "gene_name": "MKNK1", "gene_names_uniprotkb": "MKNK1; MNK1", "gene_names_refseq": "MKNK1; MNK1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of Mnk1 by caspase-activated Pak2/gamma-PAK inhibits phosphorylation and interaction of eIF4G with Mnk.", "journal": "The Journal of biological chemistry", "date": "2004", "authors": "Orton KC, Ling J, Waskiewicz AJ, Cooper JA, Merrick WC, Korneeva NL, Rhoads RE, Sonenberg N, Traugh JA", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "15234964", "url": "https://glygen.org/publication/PubMed/15234964" } ] }, { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15234964", "url": "https://glygen.org/publication/PubMed/15234964", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LPIADGDRRRKKKRRGRATD", "down_seq": "LPGKFEDMYKLTSELLGEGA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q13177-1", "kinase_gene_name": "PAK2", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" }, { "database": "PubMed", "id": "15234964", "url": "https://glygen.org/publication/PubMed/15234964" } ], "site_lbl": "Ser39" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "site_lbl": "Ser39" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "snv", "site_list": [ { "start_pos": "308", "end_pos": "308" }, { "start_pos": "402", "end_pos": "402" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "191", "end_pos": "191" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "460", "end_pos": "460" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BUB5-1.437.437", "start_pos": 437, "end_pos": 437, "uniprot_canonical_ac": "Q9BUB5-1", "length": 465, "uniprot_id": "MKNK1_HUMAN", "protein_name": "MAP kinase-interacting serine/threonine-protein kinase 1", "refseq_ac": "NP_945324", "refseq_name": "MAP kinase-interacting serine/threonine-protein kinase 1 isoform 2", "gene_name": "MKNK1", "gene_names_uniprotkb": "MKNK1; MNK1", "gene_names_refseq": "MKNK1; MNK1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Features of the catalytic domains and C termini of the MAPK signal-integrating kinases Mnk1 and Mnk2 determine their differing activities and regulatory properties.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Parra JL, Buxade M, Proud CG", "evidence": [ { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "16162500", "url": "https://glygen.org/publication/PubMed/16162500" } ] } ], "crossref": [ { "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "16162500", "url": "https://glygen.org/publication/PubMed/16162500", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BUB5", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q9BUB5", "database": "PRO", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ENELAEEPEALADGLCSMKL", "down_seq": "PPCKSRLARRRALAQAGRGE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" }, { "database": "PubMed", "id": "16162500", "url": "https://glygen.org/publication/PubMed/16162500" }, { "database": "PRO", "id": "Q9BUB5", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q9BUB5" } ], "site_lbl": "Ser437" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "snv", "site_list": [ { "start_pos": "308", "end_pos": "308" }, { "start_pos": "402", "end_pos": "402" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "191", "end_pos": "191" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "460", "end_pos": "460" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BUB5-1.460.460", "start_pos": 460, "end_pos": 460, "uniprot_canonical_ac": "Q9BUB5-1", "length": 465, "uniprot_id": "MKNK1_HUMAN", "protein_name": "MAP kinase-interacting serine/threonine-protein kinase 1", "refseq_ac": "NP_945324", "refseq_name": "MAP kinase-interacting serine/threonine-protein kinase 1 isoform 2", "gene_name": "MKNK1", "gene_names_uniprotkb": "MKNK1; MNK1", "gene_names_refseq": "MKNK1; MNK1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CKSRLARRRALAQAGRGEDR", "down_seq": "PPTAL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BUB5", "url": "https://www.uniprot.org/uniprotkb/Q9BUB5" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q9BUB5", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BUB5" } ], "site_lbl": "Ser460" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "232", "end_pos": "232" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "78", "end_pos": "78" } ] }, { "type": "snv", "site_list": [ { "start_pos": "308", "end_pos": "308" }, { "start_pos": "402", "end_pos": "402" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "191", "end_pos": "191" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "460", "end_pos": "460" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "A2RRP1-1.1750.1750", "start_pos": 1750, "end_pos": 1750, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1259835627", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1259835627", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1259835627", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1259835627#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ETLKTDPEAFHQHMVKYIYP", "down_seq": "IGGFDHERLQYYFTLLENCG", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr1750", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1259835627", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1259835627" }, { "id": "rs1259835627", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1259835627#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "2", "chr_pos": "15276992", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1750", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "A2RRP1-1.1770.1770", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.307.307", "start_pos": 307, "end_pos": 307, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "A2RRP1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2RRP1" }, { "database": "O-GlcNAc Atlas", "id": "A2RRP1", "url": "https://oglcnac.org/atlas/detail/A2RRP1" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "A2RRP1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2RRP1" }, { "database": "O-GlcNAc Atlas", "id": "A2RRP1", "url": "https://oglcnac.org/atlas/detail/A2RRP1" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "A2RRP1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2RRP1" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] } ], "crossref": [ { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "A2RRP1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2RRP1", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "A2RRP1", "url": "https://oglcnac.org/atlas/detail/A2RRP1", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1245430793", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1245430793", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1245430793", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1245430793", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs760087517", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760087517", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760087517", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760087517", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760087517", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760087517#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs760087517", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760087517", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TNGGDGVTAVPKTLGLLRML", "down_seq": "VKFYSRQGQEQDGIFKMSLS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser307", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "A2RRP1", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2RRP1" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "A2RRP1", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/A2RRP1" } ] } ], "snv": [ { "evidence": [ { "id": "rs1245430793", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1245430793" }, { "id": "rs1245430793", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1245430793" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->G).", "chr_id": "2", "chr_pos": "15504180", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S307", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760087517", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760087517" }, { "id": "rs760087517", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760087517" }, { "id": "rs760087517", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760087517#frequency_tab" }, { "id": "rs760087517", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760087517" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->I).", "chr_id": "2", "chr_pos": "15504179", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S307", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760087517", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760087517" }, { "id": "rs760087517", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760087517" }, { "id": "rs760087517", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760087517#frequency_tab" }, { "id": "rs760087517", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760087517" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->N).", "chr_id": "2", "chr_pos": "15504179", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S307", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "A2RRP1-1.887.887", "start_pos": 887, "end_pos": 887, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "A2RRP1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2RRP1" }, { "database": "O-GlcNAc Atlas", "id": "A2RRP1", "url": "https://oglcnac.org/atlas/detail/A2RRP1" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "A2RRP1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2RRP1" }, { "database": "O-GlcNAc Atlas", "id": "A2RRP1", "url": "https://oglcnac.org/atlas/detail/A2RRP1" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "A2RRP1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2RRP1" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] } ], "crossref": [ { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "A2RRP1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2RRP1", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "A2RRP1", "url": "https://oglcnac.org/atlas/detail/A2RRP1", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IRLGMERNIPGLLVLCDNLV", "down_seq": "LETLVYEARCDVTLTLKELQ", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr887", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "A2RRP1", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2RRP1" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "A2RRP1", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/A2RRP1" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "A2RRP1-1.873.873", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "A2RRP1-1.876.876", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "A2RRP1-1.900.900", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "A2RRP1-1.106.106", "start_pos": 106, "end_pos": 106, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1664476661", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1664476661", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1664476661", "url": "https://www.ensembl.org/id/rs1664476661", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KQINWHLVLASNGKLLAAVQ", "down_seq": "QCVEIRSAKDDFTSIIGKCQ", "snv": [ { "evidence": [ { "id": "rs1664476661", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1664476661" }, { "id": "rs1664476661", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1664476661" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DQC->NQC).", "chr_id": "2", "chr_pos": "15553445", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D106", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "A2RRP1-1.111.111", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1073.1073", "start_pos": 1073, "end_pos": 1073, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "HGLEKPISFVKNTQSSSEEA", "down_seq": "KLMVRLTRHTGRKQPPVSES", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "2", "chr_pos": "15394266", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1073", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1110.1110", "start_pos": 1110, "end_pos": 1110, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2528786405", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2528786405", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VSESHWRTLLQDMLTMQQNV", "down_seq": "TCLDSDACYEIFTESLLCSS", "snv": [ { "evidence": [ { "id": "rs2528786405", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2528786405" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YTC->NTC).", "chr_id": "2", "chr_pos": "15383247", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1110", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "HLVLASNGKLLAAVQDQCVE", "down_seq": "RSAKDDFTSIIGKCQVPKDP", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "I", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (IRS->NRS).", "chr_id": "2", "chr_pos": "15553429", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "I111", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "A2RRP1-1.106.106", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1215.1215", "start_pos": 1215, "end_pos": 1215, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LARCCLQLITDRPPAIQEEL", "down_seq": "LIQAVGCLEEFGVKILPLQV", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "15374668", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1215", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "A2RRP1-1.1220.1220", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1220.1220", "start_pos": 1220, "end_pos": 1220, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LQLITDRPPAIQEELDLIQA", "down_seq": "GCLEEFGVKILPLQVRLCPD", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "15374653", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V1220", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "A2RRP1-1.1215.1215", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1246.1246", "start_pos": 1246, "end_pos": 1246, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760781464", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760781464", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760781464", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760781464", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760781464", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760781464", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "FGVKILPLQVRLCPDRISLI", "down_seq": "ECISQSPTCYKQSTKLLGLA", "snv": [ { "evidence": [ { "id": "rs760781464", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760781464" }, { "id": "rs760781464", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760781464" }, { "id": "rs760781464", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760781464" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KEC->NEC).", "chr_id": "2", "chr_pos": "15366659", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1246", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1293.1293", "start_pos": 1293, "end_pos": 1293, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GENPEERRGQVLILLVEQAL", "down_seq": "FHDYKAASMHCQELMATGYP", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "4", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "15356356", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1293", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1334.1334", "start_pos": 1334, "end_pos": 1334, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KSWDVCSQLGQSEGYQDLAT", "down_seq": "QELMAFALTHCPPSSIELLL", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "2", "chr_pos": "15353641", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1334", "disease": [ { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1357.1357", "start_pos": 1357, "end_pos": 1357, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1199205096", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1199205096", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1199205096", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1199205096#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1199205096", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1199205096", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LMAFALTHCPPSSIELLLAA", "down_seq": "SSLQTEILYQRVNFQIHHEG", "snv": [ { "evidence": [ { "id": "rs1199205096", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1199205096" }, { "id": "rs1199205096", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1199205096#frequency_tab" }, { "id": "rs1199205096", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1199205096" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SSS->NSS).", "chr_id": "2", "chr_pos": "15353572", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1357", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1404.1404", "start_pos": 1404, "end_pos": 1404, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1268457533", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1268457533", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1268457533", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1268457533", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SPLTSKAVQEDEVGVPGSNS", "down_seq": "DLLRWTTATTMKVLSNTTTT", "snv": [ { "evidence": [ { "id": "rs1268457533", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1268457533" }, { "id": "rs1268457533", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1268457533" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSA->NST).", "chr_id": "2", "chr_pos": "15330735", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1404", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "A2RRP1-1.1421.1421", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1421.1421", "start_pos": 1421, "end_pos": 1421, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1437453124", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1437453124", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1437453124", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1437453124#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1437453124", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1437453124", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SNSADLLRWTTATTMKVLSN", "down_seq": "TTTTKAVLQAVSDGQWWKKS", "snv": [ { "evidence": [ { "id": "rs1437453124", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1437453124" }, { "id": "rs1437453124", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1437453124#frequency_tab" }, { "id": "rs1437453124", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1437453124" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TTT->NTT).", "chr_id": "2", "chr_pos": "15330683", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1421", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "A2RRP1-1.1404.1404", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "A2RRP1-1.1439.1439", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1439.1439", "start_pos": 1439, "end_pos": 1439, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1572668879", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572668879", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1572668879", "url": "https://www.ensembl.org/id/rs1572668879", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SNTTTTTKAVLQAVSDGQWW", "down_seq": "KSLTYLRPLQGQKCGGAYQI", "snv": [ { "evidence": [ { "id": "rs1572668879", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1572668879" }, { "id": "rs1572668879", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1572668879" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KKS->NKS).", "chr_id": "2", "chr_pos": "15330628", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1439", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "A2RRP1-1.1421.1421", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "A2RRP1-1.1456.1456", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.143.143", "start_pos": 143, "end_pos": 143, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs565228279", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs565228279", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs565228279", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs565228279", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs565228279", "url": "https://www.ncbi.nlm.nih.gov/snp/rs565228279#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs565228279", "url": "http://gnomad.broadinstitute.org/awesome?query=rs565228279", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GKCQVPKDPKPQWRRVAWSY", "down_seq": "CTLLAYAESTGTVRVFDLMG", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" }, { "id": "rs565228279", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs565228279" }, { "id": "rs565228279", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs565228279" }, { "id": "rs565228279", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs565228279#frequency_tab" }, { "id": "rs565228279", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs565228279" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DCT->NCT).", "chr_id": "2", "chr_pos": "15539309", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D143", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1456.1456", "start_pos": 1456, "end_pos": 1456, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QWWKKSLTYLRPLQGQKCGG", "down_seq": "YQIGTTANEDLEKQGCHPFY", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "15328293", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A1456", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "A2RRP1-1.1439.1439", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1540.1540", "start_pos": 1540, "end_pos": 1540, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GEVFPTTEVLLQLASEALPN", "down_seq": "MTLALAYLLALPQVLDANRC", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DMT->NMT).", "chr_id": "2", "chr_pos": "15309212", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1540", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "A2RRP1-1.1541.1541", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1541.1541", "start_pos": 1541, "end_pos": 1541, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1437588725", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1437588725", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1437588725", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1437588725", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "EVFPTTEVLLQLASEALPND", "down_seq": "TLALAYLLALPQVLDANRCF", "snv": [ { "evidence": [ { "id": "rs1437588725", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1437588725" }, { "id": "rs1437588725", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1437588725" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDM->NDT).", "chr_id": "2", "chr_pos": "15309208", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1541", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "A2RRP1-1.1540.1540", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1563.1563", "start_pos": 1563, "end_pos": 1563, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LALAYLLALPQVLDANRCFE", "down_seq": "QSPSALSLQLAAYYYSLQIY", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KQS->NQS).", "chr_id": "2", "chr_pos": "15308324", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K1563", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1612.1612", "start_pos": 1612, "end_pos": 1612, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs756163155", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756163155", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756163155", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756163155", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756163155", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756163155", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "DKCHPLYRADPKELIKMVTR", "down_seq": "VTRHEHEAWPEDLISLTKQL", "snv": [ { "evidence": [ { "id": "rs756163155", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756163155" }, { "id": "rs756163155", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756163155" }, { "id": "rs756163155", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756163155" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HVT->NVT).", "chr_id": "2", "chr_pos": "15292730", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1612", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1638.1638", "start_pos": 1638, "end_pos": 1638, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs529487212", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs529487212", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs529487212", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs529487212", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs529487212", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs529487212", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs529487212", "url": "https://www.ncbi.nlm.nih.gov/snp/rs529487212#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs529487212", "url": "http://gnomad.broadinstitute.org/awesome?query=rs529487212", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "HEAWPEDLISLTKQLHCYNE", "down_seq": "LLDFTQAQILQGLRKGVDVQ", "snv": [ { "evidence": [ { "id": "rs529487212", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs529487212" }, { "id": "rs529487212", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs529487212" }, { "id": "rs529487212", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs529487212" }, { "id": "rs529487212", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs529487212#frequency_tab" }, { "id": "rs529487212", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs529487212" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NER->NEC).", "chr_id": "2", "chr_pos": "15292652", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "R1638", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "A2RRP1-1.1641.1641", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1641.1641", "start_pos": 1641, "end_pos": 1641, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2148112814", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2148112814", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2148112814", "url": "https://www.ensembl.org/id/rs2148112814", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "WPEDLISLTKQLHCYNERLL", "down_seq": "FTQAQILQGLRKGVDVQRFT", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" }, { "id": "rs2148112814", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2148112814" }, { "id": "rs2148112814", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2148112814" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DFT->NFT).", "chr_id": "2", "chr_pos": "15292643", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1641", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "A2RRP1-1.1638.1638", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1694.1694", "start_pos": 1694, "end_pos": 1694, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs757665960", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757665960", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757665960", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757665960", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757665960", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757665960#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs757665960", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757665960", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LAETLEESVYSIAISLAQRY", "down_seq": "VSRWEVFMTHLEFLFTDSGL", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" }, { "id": "rs757665960", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757665960" }, { "id": "rs757665960", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757665960" }, { "id": "rs757665960", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757665960#frequency_tab" }, { "id": "rs757665960", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757665960" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SVS->NVS).", "chr_id": "2", "chr_pos": "15287130", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S1694", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1723.1723", "start_pos": 1723, "end_pos": 1723, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1256946075", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1256946075", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1256946075", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1256946075#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "THLEFLFTDSGLSTLEIENR", "down_seq": "QDLHLFETLKTDPEAFHQHM", "snv": [ { "evidence": [ { "id": "rs1256946075", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1256946075" }, { "id": "rs1256946075", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1256946075#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRA->NRT).", "chr_id": "2", "chr_pos": "15277073", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1723", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1770.1770", "start_pos": 1770, "end_pos": 1770, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2148058858", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2148058858", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2148058858", "url": "https://www.ensembl.org/id/rs2148058858", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "TIGGFDHERLQYYFTLLENC", "down_seq": "CADLGNCAIKPETHIRLLKK", "snv": [ { "evidence": [ { "id": "rs2148058858", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2148058858" }, { "id": "rs2148058858", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2148058858" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NCG->NCS).", "chr_id": "2", "chr_pos": "15276932", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1770", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "A2RRP1-1.1750.1750", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "A2RRP1-1.1778.1778", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "A2RRP1-1.1786.1786", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1778.1778", "start_pos": 1778, "end_pos": 1778, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs772727676", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772727676", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772727676", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772727676", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772727676", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772727676", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "RLQYYFTLLENCGCADLGNC", "down_seq": "IKPETHIRLLKKFKVVASGL", "snv": [ { "evidence": [ { "id": "rs772727676", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772727676" }, { "id": "rs772727676", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772727676" }, { "id": "rs772727676", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772727676" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NCA->NCT).", "chr_id": "2", "chr_pos": "15276908", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1778", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "A2RRP1-1.1770.1770", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "A2RRP1-1.1786.1786", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1786.1786", "start_pos": 1786, "end_pos": 1786, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LENCGCADLGNCAIKPETHI", "down_seq": "LLKKFKVVASGLNYKKLTDE", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "15276884", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1786", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "A2RRP1-1.1770.1770", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "A2RRP1-1.1778.1778", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1908.1908", "start_pos": 1908, "end_pos": 1908, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs751941601", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751941601", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751941601", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751941601", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751941601", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751941601", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "HPGDLITVVDAVTFSPKAVT", "down_seq": "LSVEARKEMTRKAIKTVKHF", "snv": [ { "evidence": [ { "id": "rs751941601", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751941601" }, { "id": "rs751941601", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751941601" }, { "id": "rs751941601", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751941601" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KLS->NLS).", "chr_id": "2", "chr_pos": "15275484", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1908", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "A2RRP1-1.1922.1922", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1922.1922", "start_pos": 1922, "end_pos": 1922, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs754580352", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754580352", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs754580352", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754580352", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs754580352", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754580352#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs754580352", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754580352", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "SPKAVTKLSVEARKEMTRKA", "down_seq": "KTVKHFIEKPRKRNSEDEAQ", "snv": [ { "evidence": [ { "id": "rs754580352", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754580352" }, { "id": "rs754580352", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754580352" }, { "id": "rs754580352", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754580352#frequency_tab" }, { "id": "rs754580352", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754580352" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IKT->NKT).", "chr_id": "2", "chr_pos": "15238646", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1922", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "A2RRP1-1.1908.1908", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.192.192", "start_pos": 192, "end_pos": 192, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs751941818", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751941818", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751941818", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751941818", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751941818", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751941818#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs751941818", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751941818", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ASSFIGDLSYAIAGLIFLEY", "down_seq": "ASAQWSAELLVINYRGELRS", "snv": [ { "evidence": [ { "id": "rs751941818", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751941818" }, { "id": "rs751941818", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751941818" }, { "id": "rs751941818", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751941818#frequency_tab" }, { "id": "rs751941818", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751941818" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KAS->NAS).", "chr_id": "2", "chr_pos": "15536489", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K192", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "A2RRP1-1.207.207", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.1945.1945", "start_pos": 1945, "end_pos": 1945, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2528288665", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2528288665", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VKHFIEKPRKRNSEDEAQEA", "down_seq": "DSKVTYADTLNHLEKSLAHL", "snv": [ { "evidence": [ { "id": "rs2528288665", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2528288665" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KDS->NDS).", "chr_id": "2", "chr_pos": "15238576", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1945", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.2030.2030", "start_pos": 2030, "end_pos": 2030, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs777142694", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777142694", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777142694", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777142694", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777142694", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777142694", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LDGQPLAMIQQLLEVAVGPL", "down_seq": "ISPKDIVQSAIMKIISALSG", "snv": [ { "evidence": [ { "id": "rs777142694", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777142694" }, { "id": "rs777142694", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777142694" }, { "id": "rs777142694", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777142694" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DIS->NIS).", "chr_id": "2", "chr_pos": "15234603", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D2030", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.207.207", "start_pos": 207, "end_pos": 207, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IFLEYKASAQWSAELLVINY", "down_seq": "GELRSYLVSVGTNQSYQESH", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "15536446", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R207", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "A2RRP1-1.192.192", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.2196.2196", "start_pos": 2196, "end_pos": 2196, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1323025608", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1323025608", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1323025608", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1323025608", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LVLLLQAWPPMKSEYVITNN", "down_seq": "WVRLATVMLTRCTMENKEGL", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NNP->NNS).", "chr_id": "2", "chr_pos": "15186867", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P2196", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1323025608", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1323025608" }, { "id": "rs1323025608", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1323025608" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNP->NNT).", "chr_id": "2", "chr_pos": "15186867", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P2196", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "A2RRP1-1.2212.2212", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.2212.2212", "start_pos": 2212, "end_pos": 2212, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ITNNPWVRLATVMLTRCTME", "down_seq": "KEGLGNEVLKMCRSLYNTKQ", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "15186817", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "N2212", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "A2RRP1-1.2196.2196", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "A2RRP1-1.2225.2225", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.2225.2225", "start_pos": 2225, "end_pos": 2225, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LTRCTMENKEGLGNEVLKMC", "down_seq": "SLYNTKQMLPAEGVKELCLL", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "15186780", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R2225", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "A2RRP1-1.2212.2212", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.2263.2263", "start_pos": 2263, "end_pos": 2263, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "CLLLLNQSLLLPSLKLLLES", "down_seq": "DEHLHEMALEQITAVTTVND", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "15179041", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R2263", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.2359.2359", "start_pos": 2359, "end_pos": 2359, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs376484930", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376484930", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs376484930", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376484930", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs376484930", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376484930#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs376484930", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376484930", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HEAEAGSLLLAVRGTHQAFR", "down_seq": "FSTALRAAQHWV", "snv": [ { "evidence": [ { "id": "rs376484930", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376484930" }, { "id": "rs376484930", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376484930" }, { "id": "rs376484930", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376484930#frequency_tab" }, { "id": "rs376484930", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376484930" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TFS->NFS).", "chr_id": "2", "chr_pos": "15167088", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2359", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.242.242", "start_pos": 242, "end_pos": 242, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1262214723", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1262214723", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1262214723", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1262214723#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1262214723", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1262214723", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SYQESHCFSFSSHYPHGINT", "down_seq": "IYHPGHRLLLVGGCETAEVG", "snv": [ { "evidence": [ { "id": "rs1262214723", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1262214723" }, { "id": "rs1262214723", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1262214723#frequency_tab" }, { "id": "rs1262214723", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1262214723" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTA->NTT).", "chr_id": "2", "chr_pos": "15534565", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A242", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.411.411", "start_pos": 411, "end_pos": 411, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1680165803", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1680165803", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1680165803", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1680165803#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IDVNWWADSAVTLARCSGAL", "down_seq": "VSSVKTLKNLLGKSCEWFEP", "snv": [ { "evidence": [ { "id": "rs1680165803", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1680165803" }, { "id": "rs1680165803", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1680165803#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TVS->NVS).", "chr_id": "2", "chr_pos": "15475796", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T411", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.455.455", "start_pos": 455, "end_pos": 455, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1680092734", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1680092734", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1680092734", "url": "https://www.ensembl.org/id/rs1680092734", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VTATHDGGFLSLECEIKLAP", "down_seq": "RSRLETRAGEEDEGEEDSDS", "snv": [ { "evidence": [ { "id": "rs1680092734", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1680092734" }, { "id": "rs1680092734", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1680092734" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KRS->NRS).", "chr_id": "2", "chr_pos": "15474301", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K455", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "A2RRP1-1.458.458", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "A2RRP1-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "A2RRP1-1.475.475", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.458.458", "start_pos": 458, "end_pos": 458, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "THDGGFLSLECEIKLAPKRS", "down_seq": "LETRAGEEDEGEEDSDSDYE", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "15474294", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R458", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "A2RRP1-1.455.455", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "A2RRP1-1.473.473", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "A2RRP1-1.475.475", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.517.517", "start_pos": 517, "end_pos": 517, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs370526257", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370526257", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs370526257", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370526257", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs370526257", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370526257#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs370526257", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370526257", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TEMERFAPPRKRPRTITKNY", "down_seq": "LVSLRSTTPEELYQRKIESE", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" }, { "id": "rs370526257", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370526257" }, { "id": "rs370526257", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370526257" }, { "id": "rs370526257", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370526257#frequency_tab" }, { "id": "rs370526257", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370526257" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NYR->NYC).", "chr_id": "2", "chr_pos": "15474117", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R517", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:0080778", "recommended_name": { "id": "DOID:0080778", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080778", "name": "transient infantile liver failure", "description": "A liver disease that is characterized by elevated liver enzymes, jaundice, vomiting, coagulopathy, and hyperbilirubinemia, and the presence of increased serum lactate and that has_material_basis_in homozygous or compound heterozygous mutation in the TRMU gene, which is involved in mitochondrial protein translation, on chromosome 22q13." }, "synonyms": [ { "id": "MONDO:0013111", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013111", "name": "acute infantile liver failure due to synthesis defect of mtDNA-encoded proteins", "description": "Acute infantile liver failure due to mtDNA-encoded proteins synthesis defect is a very rare mitochondrial respiratory chain deficiency described in fewer than 10 infants, primarily of middle Eastern descent, and characterized clinically by transient but life-threatening liver failure with elevated liver enzymes, jaundice, vomiting, coagulopathy, hyperbilirubinemia, and lactic acidemia." }, { "id": "MONDO:0013111", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013111", "name": "acute infantile liver failure", "description": "" }, { "id": "MONDO:0013111", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013111", "name": "LFIT", "description": "" }, { "id": "MONDO:0013111", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013111", "name": "TRMU infantile liver failure", "description": "" }, { "id": "MONDO:0013111", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013111", "name": "acute infantile liver failure due to synthesis defect of mitochondrial DNA-encoded proteins", "description": "" }, { "id": "MONDO:0013111", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013111", "name": "acute infantile liver failure due to synthesis defect of mtDNA-encoded proteins", "description": "" }, { "id": "MONDO:0013111", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013111", "name": "infantile liver failure caused by mutation in TRMU", "description": "" }, { "id": "MONDO:0013111", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013111", "name": "liver failure, infantile, transient", "description": "" }, { "id": "MONDO:0013111", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013111", "name": "liver failure, transient infantile", "description": "" }, { "id": "MONDO:0013111", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013111", "name": "transient infantile liver failure", "description": "" }, { "id": "MIM:613070", "resource": "MIM", "url": "https://www.omim.org/entry/613070", "name": "Liver failure, infantile, transient", "description": "Liver failure, infantile, transient" } ], "unlinked_id_list": [], "evidence": [ { "id": "613070", "database": "MIM", "url": "https://www.omim.org/entry/613070" }, { "id": "0080778", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080778" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "A2RRP1-1.511.511", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.569.569", "start_pos": 569, "end_pos": 569, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "YGLDTDLVYQRQWRKSAVNV", "down_seq": "SIQNYLSKIKKRSWVLHECL", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NVA->NVS).", "chr_id": "2", "chr_pos": "15473242", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A569", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "A2RRP1-1.574.574", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.574.574", "start_pos": 574, "end_pos": 574, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1225879842", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225879842", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1225879842", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1225879842#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1225879842", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1225879842", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DLVYQRQWRKSAVNVASIQN", "down_seq": "LSKIKKRSWVLHECLERVPE", "snv": [ { "evidence": [ { "id": "rs1225879842", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225879842" }, { "id": "rs1225879842", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1225879842#frequency_tab" }, { "id": "rs1225879842", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1225879842" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YLS->NLS).", "chr_id": "2", "chr_pos": "15473227", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y574", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "A2RRP1-1.569.569", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.637.637", "start_pos": 637, "end_pos": 637, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1479823236", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1479823236", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1479823236", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1479823236#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1479823236", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1479823236", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AIGKGADDGRFTLPGEIDID", "down_seq": "ISYEELSPPDEEPAKNKKEK", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" }, { "id": "rs1479823236", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1479823236" }, { "id": "rs1479823236", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1479823236#frequency_tab" }, { "id": "rs1479823236", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1479823236" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SIS->NIS).", "chr_id": "2", "chr_pos": "15467772", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S637", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "A2RRP1-1.640.640", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.640.640", "start_pos": 640, "end_pos": 640, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "KGADDGRFTLPGEIDIDSIS", "down_seq": "EELSPPDEEPAKNKKEKELK", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "Y", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "2", "chr_pos": "15467763", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "Y640", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "A2RRP1-1.637.637", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.673.673", "start_pos": 673, "end_pos": 673, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753412601", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753412601", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753412601", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753412601", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753412601", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753412601", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "NKKEKELKKRQELLKLVNFS", "down_seq": "LTLEQKELCRCRRKLLTYLD", "snv": [ { "evidence": [ { "id": "rs753412601", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753412601" }, { "id": "rs753412601", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753412601" }, { "id": "rs753412601", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753412601" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KLT->NLT).", "chr_id": "2", "chr_pos": "15467407", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K673", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.72.72", "start_pos": 72, "end_pos": 72, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "ITKAIRDRLLFLRQYIWYSP", "down_seq": "PFLLPDGLVRLVNKQINWHL", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "2", "chr_pos": "15554134", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A72", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.748.748", "start_pos": 748, "end_pos": 748, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "SARTYAQESNVQALEILFTY", "down_seq": "GSDLLPHRLAILSNFPETTS", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (HGS->NGS).", "chr_id": "2", "chr_pos": "15461298", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H748", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "A2RRP1-1.749.749", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "A2RRP1-1.764.764", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "A2RRP1-1.766.766", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.749.749", "start_pos": 749, "end_pos": 749, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "ARTYAQESNVQALEILFTYH", "down_seq": "SDLLPHRLAILSNFPETTSP", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "15461294", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G749", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "A2RRP1-1.748.748", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "A2RRP1-1.764.764", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "A2RRP1-1.766.766", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.764.764", "start_pos": 764, "end_pos": 764, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200532922", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200532922", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200532922", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200532922", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200532922", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200532922#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200532922", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200532922", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LFTYHGSDLLPHRLAILSNF", "down_seq": "ETTSPHEYSVLLPEACFNGD", "snv": [ { "evidence": [ { "id": "rs200532922", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200532922" }, { "id": "rs200532922", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200532922" }, { "id": "rs200532922", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200532922#frequency_tab" }, { "id": "rs200532922", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200532922" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFP->NFS).", "chr_id": "2", "chr_pos": "15461250", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P764", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "A2RRP1-1.748.748", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "A2RRP1-1.749.749", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "A2RRP1-1.766.766", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.766.766", "start_pos": 766, "end_pos": 766, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs771882591", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771882591", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771882591", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs771882591", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs771882591", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771882591", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771882591", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771882591#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771882591", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771882591", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TYHGSDLLPHRLAILSNFPE", "down_seq": "TSPHEYSVLLPEACFNGDSL", "snv": [ { "evidence": [ { "id": "rs771882591", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771882591" }, { "id": "rs771882591", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs771882591" }, { "id": "rs771882591", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771882591" }, { "id": "rs771882591", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771882591#frequency_tab" }, { "id": "rs771882591", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771882591" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TTS->NTS).", "chr_id": "2", "chr_pos": "15417510", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T766", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "A2RRP1-1.748.748", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "A2RRP1-1.749.749", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "A2RRP1-1.764.764", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.817.817", "start_pos": 817, "end_pos": 817, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1216893226", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1216893226", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1216893226", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1216893226", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "RAKDWCEELACRMVVEPNLQ", "down_seq": "ESEFLYAAQPELLRFRMTQL", "snv": [ { "evidence": [ { "id": "rs1216893226", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1216893226" }, { "id": "rs1216893226", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1216893226" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DES->NES).", "chr_id": "2", "chr_pos": "15424443", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D817", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.838.838", "start_pos": 838, "end_pos": 838, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ESEFLYAAQPELLRFRMTQL", "down_seq": "VEKVMDWYQTRAEEIEHYAR", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "15424379", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T838", "disease": [ { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.873.873", "start_pos": 873, "end_pos": 873, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IEHYARQVDCALSLIRLGME", "down_seq": "NIPGLLVLCDNLVTLETLVY", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "15417672", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R873", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "A2RRP1-1.876.876", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "A2RRP1-1.887.887", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.876.876", "start_pos": 876, "end_pos": 876, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1677011377", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1677011377", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1677011377", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1677011377", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "YARQVDCALSLIRLGMERNI", "down_seq": "GLLVLCDNLVTLETLVYEAR", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" }, { "id": "rs1677011377", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1677011377" }, { "id": "rs1677011377", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1677011377" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NIP->NIS).", "chr_id": "2", "chr_pos": "15417664", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P876", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "A2RRP1-1.873.873", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "A2RRP1-1.887.887", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.900.900", "start_pos": 900, "end_pos": 900, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RRP1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VLCDNLVTLETLVYEARCDV", "down_seq": "LTLKELQQMKDIEKLRLLMN", "snv": [ { "evidence": [ { "id": "A2RRP1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RRP1" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TLT->NLT).", "chr_id": "2", "chr_pos": "15417591", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T900", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "A2RRP1-1.887.887", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2RRP1-1.2052.2052", "start_pos": 2052, "end_pos": 2052, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "A2RRP1-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "A2RRP1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPKDIVQSAIMKIISALSGG", "down_seq": "ADLGGPRDPLKVLEGVVAAV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "A2RRP1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser2052" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "A2RRP1-1.473.473", "start_pos": 473, "end_pos": 473, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" }, { "database": "iPTMnet", "id": "A2RRP1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "title": "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.", "journal": "Journal of proteomics", "date": "2014", "authors": "Bian Y, Song C, Cheng K, Dong M, Wang F, Huang J, Sun D, Wang L, Ye M, Zou H", "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" }, { "database": "iPTMnet", "id": "A2RRP1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" }, { "database": "iPTMnet", "id": "A2RRP1-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.", "journal": "Science signaling", "date": "2009", "authors": "Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK", "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" }, { "database": "iPTMnet", "id": "A2RRP1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" }, { "database": "iPTMnet", "id": "A2RRP1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Motif-specific sampling of phosphoproteomes.", "journal": "Journal of proteome research", "date": "2008", "authors": "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "evidence": [ { "database": "iPTMnet", "id": "A2RRP1-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "Phosphoproteome analysis of the human Chang liver cells using SCX and a complementary mass spectrometric strategy.", "journal": "Proteomics", "date": "2008", "authors": "Sui S, Wang J, Yang B, Song L, Zhang J, Chen M, Liu J, Lu Z, Cai Y, Chen S, Bi W, Zhu Y, He F, Qian X", "evidence": [ { "database": "iPTMnet", "id": "A2RRP1-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1-1" } ], "reference": [ { "type": "PubMed", "id": "18491316", "url": "https://glygen.org/publication/PubMed/18491316" } ] }, { "title": "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Pan C, Olsen JV, Daub H, Mann M", "evidence": [ { "database": "iPTMnet", "id": "A2RRP1-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Phosphoproteome analysis of human liver tissue by long-gradient nanoflow LC coupled with multiple stage MS analysis.", "journal": "Electrophoresis", "date": "2010", "authors": "Han G, Ye M, Liu H, Song C, Sun D, Wu Y, Jiang X, Chen R, Wang C, Wang L, Zou H", "evidence": [ { "database": "iPTMnet", "id": "A2RRP1-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1-1" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "A2RRP1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18491316", "url": "https://glygen.org/publication/PubMed/18491316", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "APKRSRLETRAGEEDEGEED", "down_seq": "DSDYEISAKARYFGYIKQGL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "A2RRP1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "18491316", "url": "https://glygen.org/publication/PubMed/18491316" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Ser473" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "A2RRP1-1.455.455", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "A2RRP1-1.458.458", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "A2RRP1-1.475.475", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "A2RRP1-1.475.475", "start_pos": 475, "end_pos": 475, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" }, { "database": "iPTMnet", "id": "A2RRP1-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" }, { "database": "iPTMnet", "id": "A2RRP1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "title": "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.", "journal": "Science signaling", "date": "2009", "authors": "Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK", "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" }, { "database": "iPTMnet", "id": "A2RRP1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "title": "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.", "journal": "Journal of proteomics", "date": "2014", "authors": "Bian Y, Song C, Cheng K, Dong M, Wang F, Huang J, Sun D, Wang L, Ye M, Zou H", "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" }, { "database": "iPTMnet", "id": "A2RRP1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "title": "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Pan C, Olsen JV, Daub H, Mann M", "evidence": [ { "database": "iPTMnet", "id": "A2RRP1-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Phosphoproteome analysis of human liver tissue by long-gradient nanoflow LC coupled with multiple stage MS analysis.", "journal": "Electrophoresis", "date": "2010", "authors": "Han G, Ye M, Liu H, Song C, Sun D, Wu Y, Jiang X, Chen R, Wang C, Wang L, Zou H", "evidence": [ { "database": "iPTMnet", "id": "A2RRP1-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1-1" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "A2RRP1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KRSRLETRAGEEDEGEEDSD", "down_seq": "DYEISAKARYFGYIKQGLYL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "A2RRP1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Ser475" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "A2RRP1-1.455.455", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "A2RRP1-1.458.458", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "A2RRP1-1.473.473", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "A2RRP1-1.511.511", "start_pos": 511, "end_pos": 511, "uniprot_canonical_ac": "A2RRP1-1", "length": 2371, "uniprot_id": "NBAS_HUMAN", "protein_name": "NBAS subunit of NRZ tethering complex", "refseq_ac": "NP_056993", "refseq_name": "NBAS subunit of NRZ tethering complex", "gene_name": "NBAS", "gene_names_uniprotkb": "NBAS; NAG", "gene_names_refseq": "ILFS2; NAG; NBAS; SOPH", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RRP1", "url": "https://www.uniprot.org/uniprotkb/A2RRP1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "A2RRP1-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "A2RRP1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QGLYLVTEMERFAPPRKRPR", "down_seq": "ITKNYRLVSLRSTTPEELYQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "A2RRP1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RRP1" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr511" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "887", "end_pos": "887" } ] }, { "type": "snv", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1110", "end_pos": "1110" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "1215", "end_pos": "1215" }, { "start_pos": "1220", "end_pos": "1220" }, { "start_pos": "1246", "end_pos": "1246" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1334", "end_pos": "1334" }, { "start_pos": "1357", "end_pos": "1357" }, { "start_pos": "1404", "end_pos": "1404" }, { "start_pos": "1421", "end_pos": "1421" }, { "start_pos": "1439", "end_pos": "1439" }, { "start_pos": "143", "end_pos": "143" }, { "start_pos": "1456", "end_pos": "1456" }, { "start_pos": "1540", "end_pos": "1540" }, { "start_pos": "1541", "end_pos": "1541" }, { "start_pos": "1563", "end_pos": "1563" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1638", "end_pos": "1638" }, { "start_pos": "1641", "end_pos": "1641" }, { "start_pos": "1694", "end_pos": "1694" }, { "start_pos": "1723", "end_pos": "1723" }, { "start_pos": "1750", "end_pos": "1750" }, { "start_pos": "1770", "end_pos": "1770" }, { "start_pos": "1778", "end_pos": "1778" }, { "start_pos": "1786", "end_pos": "1786" }, { "start_pos": "1908", "end_pos": "1908" }, { "start_pos": "1922", "end_pos": "1922" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "1945", "end_pos": "1945" }, { "start_pos": "2030", "end_pos": "2030" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "2196", "end_pos": "2196" }, { "start_pos": "2212", "end_pos": "2212" }, { "start_pos": "2225", "end_pos": "2225" }, { "start_pos": "2263", "end_pos": "2263" }, { "start_pos": "2359", "end_pos": "2359" }, { "start_pos": "242", "end_pos": "242" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "455", "end_pos": "455" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "569", "end_pos": "569" }, { "start_pos": "574", "end_pos": "574" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "640", "end_pos": "640" }, { "start_pos": "673", "end_pos": "673" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "748", "end_pos": "748" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "876", "end_pos": "876" }, { "start_pos": "900", "end_pos": "900" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "2052", "end_pos": "2052" }, { "start_pos": "473", "end_pos": "473" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "511", "end_pos": "511" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "A2RRP1-1.517.517", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q5VZ52-1.121.121", "start_pos": 121, "end_pos": 121, "uniprot_canonical_ac": "Q5VZ52-1", "length": 161, "uniprot_id": "MORN5_HUMAN", "protein_name": "MORN repeat-containing protein 5", "refseq_ac": "NP_940871", "refseq_name": "MORN repeat-containing protein 5 isoform a", "gene_name": "MORN5", "gene_names_uniprotkb": "MORN5; C9orf113; C9orf18", "gene_names_refseq": "C9orf113; C9orf18; MORN5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VZ52", "url": "https://www.uniprot.org/uniprotkb/Q5VZ52" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VZ52", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VZ52", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "PAGMAQLTNMDPPRKIPKGY", "down_seq": "DCGDGFYNPVTRVVKDYRNR", "snv": [ { "evidence": [ { "id": "Q5VZ52", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VZ52" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "Y", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "9", "chr_pos": "122174551", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Y121", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q5VZ52-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q5VZ52-1.141.141", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5VZ52-1.125.125", "start_pos": 125, "end_pos": 125, "uniprot_canonical_ac": "Q5VZ52-1", "length": 161, "uniprot_id": "MORN5_HUMAN", "protein_name": "MORN repeat-containing protein 5", "refseq_ac": "NP_940871", "refseq_name": "MORN repeat-containing protein 5 isoform a", "gene_name": "MORN5", "gene_names_uniprotkb": "MORN5; C9orf113; C9orf18", "gene_names_refseq": "C9orf113; C9orf18; MORN5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VZ52", "url": "https://www.uniprot.org/uniprotkb/Q5VZ52" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VZ52", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VZ52", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AQLTNMDPPRKIPKGYYDCG", "down_seq": "GFYNPVTRVVKDYRNRFLRN", "snv": [ { "evidence": [ { "id": "Q5VZ52", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VZ52" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "D", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "9", "chr_pos": "122174563", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D125", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q5VZ52-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q5VZ52-1.141.141", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5VZ52-1.141.141", "start_pos": 141, "end_pos": 141, "uniprot_canonical_ac": "Q5VZ52-1", "length": 161, "uniprot_id": "MORN5_HUMAN", "protein_name": "MORN repeat-containing protein 5", "refseq_ac": "NP_940871", "refseq_name": "MORN repeat-containing protein 5 isoform a", "gene_name": "MORN5", "gene_names_uniprotkb": "MORN5; C9orf113; C9orf18", "gene_names_refseq": "C9orf113; C9orf18; MORN5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VZ52", "url": "https://www.uniprot.org/uniprotkb/Q5VZ52" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VZ52", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VZ52", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "YDCGDGFYNPVTRVVKDYRN", "down_seq": "FLRNADDDEHEWITRTCRKG", "snv": [ { "evidence": [ { "id": "Q5VZ52", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VZ52" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "9", "chr_pos": "122174610", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R141", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q5VZ52-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q5VZ52-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q5VZ52-1.159.159", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5VZ52-1.159.159", "start_pos": 159, "end_pos": 159, "uniprot_canonical_ac": "Q5VZ52-1", "length": 161, "uniprot_id": "MORN5_HUMAN", "protein_name": "MORN repeat-containing protein 5", "refseq_ac": "NP_940871", "refseq_name": "MORN repeat-containing protein 5 isoform a", "gene_name": "MORN5", "gene_names_uniprotkb": "MORN5; C9orf113; C9orf18", "gene_names_refseq": "C9orf113; C9orf18; MORN5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VZ52", "url": "https://www.uniprot.org/uniprotkb/Q5VZ52" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VZ52", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VZ52", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RNRFLRNADDDEHEWITRTC", "down_seq": "KG", "snv": [ { "evidence": [ { "id": "Q5VZ52", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VZ52" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "122199921", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R159", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q5VZ52-1.141.141", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5VZ52-1.55.55", "start_pos": 55, "end_pos": 55, "uniprot_canonical_ac": "Q5VZ52-1", "length": 161, "uniprot_id": "MORN5_HUMAN", "protein_name": "MORN repeat-containing protein 5", "refseq_ac": "NP_940871", "refseq_name": "MORN repeat-containing protein 5 isoform a", "gene_name": "MORN5", "gene_names_uniprotkb": "MORN5; C9orf113; C9orf18", "gene_names_refseq": "C9orf113; C9orf18; MORN5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VZ52", "url": "https://www.uniprot.org/uniprotkb/Q5VZ52" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VZ52", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VZ52", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MKDGMFHGEGTLYFPSGSQY", "down_seq": "AIWENGLAIKGTYTFSDGLH", "snv": [ { "evidence": [ { "id": "Q5VZ52", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VZ52" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "122166883", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D55", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q5VZ52-1.56.56", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q5VZ52-1.56.56", "start_pos": 56, "end_pos": 56, "uniprot_canonical_ac": "Q5VZ52-1", "length": 161, "uniprot_id": "MORN5_HUMAN", "protein_name": "MORN repeat-containing protein 5", "refseq_ac": "NP_940871", "refseq_name": "MORN repeat-containing protein 5 isoform a", "gene_name": "MORN5", "gene_names_uniprotkb": "MORN5; C9orf113; C9orf18", "gene_names_refseq": "C9orf113; C9orf18; MORN5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q5VZ52", "url": "https://www.uniprot.org/uniprotkb/Q5VZ52" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q5VZ52", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VZ52", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "KDGMFHGEGTLYFPSGSQYD", "down_seq": "IWENGLAIKGTYTFSDGLHY", "snv": [ { "evidence": [ { "id": "Q5VZ52", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q5VZ52" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "122166886", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A56", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q5VZ52-1.55.55", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H239-1.164.164", "start_pos": 164, "end_pos": 164, "uniprot_canonical_ac": "Q9H239-1", "length": 520, "uniprot_id": "MMP28_HUMAN", "protein_name": "Matrix metalloproteinase-28", "refseq_ac": "NP_001027449", "refseq_name": "matrix metalloproteinase-28 isoform 3 precursor", "gene_name": "MMP28", "gene_names_uniprotkb": "MMP28; MMP25; PRO4339", "gene_names_refseq": "EPILYSIN; MM28; MMP-25; MMP-28; MMP28", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H239", "url": "https://www.uniprot.org/uniprotkb/Q9H239" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H239", "url": "https://www.uniprot.org/uniprotkb/Q9H239", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "EHLPEPAVRGAVRAAFQLWS", "down_seq": "VSALEFWEAPATGPADIRLT", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn164", "evidence": [ { "id": "Q9H239", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9H239#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "43", "end_pos": "52" }, { "start_pos": "91", "end_pos": "105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "58", "end_pos": "58" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H239-1.355.355", "start_pos": 355, "end_pos": 355, "uniprot_canonical_ac": "Q9H239-1", "length": 520, "uniprot_id": "MMP28_HUMAN", "protein_name": "Matrix metalloproteinase-28", "refseq_ac": "NP_001027449", "refseq_name": "matrix metalloproteinase-28 isoform 3 precursor", "gene_name": "MMP28", "gene_names_uniprotkb": "MMP28; MMP25; PRO4339", "gene_names_refseq": "EPILYSIN; MM28; MMP-25; MMP-28; MMP28", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H239", "url": "https://www.uniprot.org/uniprotkb/Q9H239" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "Q9H239", "url": "https://www.uniprot.org/uniprotkb/Q9H239", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs376963669", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376963669", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs376963669", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376963669", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs376963669", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376963669#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs376963669", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376963669", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RQQQLYIFKGSHFWEVAADG", "down_seq": "VSEPRPLQERWVGLPPNIEA", "glycosylation": [ { "glytoucan_ac": "G28077HW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GSHFWEVAADGNVSEPR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn355", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn355", "evidence": [ { "id": "Q9H239", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q9H239#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs376963669", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376963669" }, { "id": "rs376963669", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376963669" }, { "id": "rs376963669", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376963669#frequency_tab" }, { "id": "rs376963669", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376963669" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVS->KVS).", "chr_id": "17", "chr_pos": "35767855", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N355", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "43", "end_pos": "52" }, { "start_pos": "91", "end_pos": "105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "58", "end_pos": "58" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q9H239-1.357.357", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9H239-1.43.52", "start_pos": 43, "end_pos": 52, "uniprot_canonical_ac": "Q9H239-1", "length": 520, "uniprot_id": "MMP28_HUMAN", "protein_name": "Matrix metalloproteinase-28", "refseq_ac": "NP_001027449", "refseq_name": "matrix metalloproteinase-28 isoform 3 precursor", "gene_name": "MMP28", "gene_names_uniprotkb": "MMP28; MMP25; PRO4339", "gene_names_refseq": "EPILYSIN; MM28; MMP-25; MMP-28; MMP28", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H239", "url": "https://www.uniprot.org/uniprotkb/Q9H239" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology.", "journal": "The EMBO journal", "date": "2013", "authors": "Steentoft C, Vakhrushev SY, Joshi HJ, Kong Y, Vester-Christensen MB, Schjoldager KT, Lavrsen K, Dabelsteen S, Pedersen NB, Marcos-Silva L, Gupta R, Bennett EP, Mandel U, Brunak S, Wandall HH, Levery SB, Clausen H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533" } ] }, { "title": "Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology", "journal": "EMBO J", "date": "2013", "authors": "Steentoft C., Vakhrushev S.Y., Joshi H.J., Kong Y., Vester-Christensen M.B., Schjoldager K.T., Lavrsen K., Dabelsteen S., Pedersen N.B., Marcos-Silva L., Gupta R., Bennett E.P., Mandel U., Brunak S., Wandall H.H., Levery S.B., Clausen H.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "crossref": [ { "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] } ], "site_seq": "YGYLNEQVPK", "start_aa": "Y", "up_seq": "QPAERGGQELRKEAEAFLEK", "down_seq": "APTSTRFSDAIRAFQWVSQL", "glycosylation": [ { "glytoucan_ac": "G57321FI", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YGYLNEQVPK", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Tyr", "end_aa": "Lys", "evidence": [ { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "43", "end_pos": "52" }, { "start_pos": "91", "end_pos": "105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "58", "end_pos": "58" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q9H239-1.58.58", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9H239-1.91.105", "start_pos": 91, "end_pos": 105, "uniprot_canonical_ac": "Q9H239-1", "length": 520, "uniprot_id": "MMP28_HUMAN", "protein_name": "Matrix metalloproteinase-28", "refseq_ac": "NP_001027449", "refseq_name": "matrix metalloproteinase-28 isoform 3 precursor", "gene_name": "MMP28", "gene_names_uniprotkb": "MMP28; MMP25; PRO4339", "gene_names_refseq": "EPILYSIN; MM28; MMP-25; MMP-28; MMP28", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H239", "url": "https://www.uniprot.org/uniprotkb/Q9H239" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology.", "journal": "The EMBO journal", "date": "2013", "authors": "Steentoft C, Vakhrushev SY, Joshi HJ, Kong Y, Vester-Christensen MB, Schjoldager KT, Lavrsen K, Dabelsteen S, Pedersen NB, Marcos-Silva L, Gupta R, Bennett EP, Mandel U, Brunak S, Wandall HH, Levery SB, Clausen H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533" } ] }, { "title": "Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology", "journal": "EMBO J", "date": "2013", "authors": "Steentoft C., Vakhrushev S.Y., Joshi H.J., Kong Y., Vester-Christensen M.B., Schjoldager K.T., Lavrsen K., Dabelsteen S., Pedersen N.B., Marcos-Silva L., Gupta R., Bennett E.P., Mandel U., Brunak S., Wandall H.H., Levery S.B., Clausen H.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "crossref": [ { "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] } ], "site_seq": "CGVTDTNSYAAWAER", "start_aa": "C", "up_seq": "QLPVSGVLDRATLRQMTRPR", "down_seq": "ISDLFARHRTKMRRKKRFAK", "glycosylation": [ { "glytoucan_ac": "G57321FI", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CGVTDTNSYAAWAER", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Cys", "end_aa": "Arg", "evidence": [ { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "43", "end_pos": "52" }, { "start_pos": "91", "end_pos": "105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "58", "end_pos": "58" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9H239-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q9H239-1", "length": 520, "uniprot_id": "MMP28_HUMAN", "protein_name": "Matrix metalloproteinase-28", "refseq_ac": "NP_001027449", "refseq_name": "matrix metalloproteinase-28 isoform 3 precursor", "gene_name": "MMP28", "gene_names_uniprotkb": "MMP28; MMP25; PRO4339", "gene_names_refseq": "EPILYSIN; MM28; MMP-25; MMP-28; MMP28", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H239", "url": "https://www.uniprot.org/uniprotkb/Q9H239" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "FBXO31-mediated ubiquitination of OGT maintains O-GlcNAcylation homeostasis to restrain endometrial malignancy.", "journal": "Nature communications", "date": "2025-02-02", "authors": "Zhang Na, Meng Yang, Mao Song, Ni Huiling, Huang Canhua, Shen Licong, Fu Kun, Lv Lu, Yu Chunhong, Meekrathok Piyanat, Kuang Chunmei, Chen Fang, Zhang Yu, Yuan Kai", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q9H239", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H239" } ], "reference": [ { "type": "PubMed", "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887" } ] } ], "crossref": [ { "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9H239", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H239", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "39894887", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39894887" }, { "id": "Q9H239", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H239" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "43", "end_pos": "52" }, { "start_pos": "91", "end_pos": "105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "58", "end_pos": "58" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9H239-1.130.130", "start_pos": 130, "end_pos": 130, "uniprot_canonical_ac": "Q9H239-1", "length": 520, "uniprot_id": "MMP28_HUMAN", "protein_name": "Matrix metalloproteinase-28", "refseq_ac": "NP_001027449", "refseq_name": "matrix metalloproteinase-28 isoform 3 precursor", "gene_name": "MMP28", "gene_names_uniprotkb": "MMP28; MMP25; PRO4339", "gene_names_refseq": "EPILYSIN; MM28; MMP-25; MMP-28; MMP28", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H239", "url": "https://www.uniprot.org/uniprotkb/Q9H239" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1555606647", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555606647", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1555606647", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1555606647", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "FARHRTKMRRKKRFAKQGNK", "down_seq": "YKQHLSYRLVNWPEHLPEPA", "snv": [ { "evidence": [ { "id": "rs1555606647", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555606647" }, { "id": "rs1555606647", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1555606647" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "W", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKW->NKC).", "chr_id": "17", "chr_pos": "35773394", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W130", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "43", "end_pos": "52" }, { "start_pos": "91", "end_pos": "105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "58", "end_pos": "58" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H239-1.198.198", "start_pos": 198, "end_pos": 198, "uniprot_canonical_ac": "Q9H239-1", "length": 520, "uniprot_id": "MMP28_HUMAN", "protein_name": "Matrix metalloproteinase-28", "refseq_ac": "NP_001027449", "refseq_name": "matrix metalloproteinase-28 isoform 3 precursor", "gene_name": "MMP28", "gene_names_uniprotkb": "MMP28; MMP25; PRO4339", "gene_names_refseq": "EPILYSIN; MM28; MMP-25; MMP-28; MMP28", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H239", "url": "https://www.uniprot.org/uniprotkb/Q9H239" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs759605469", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759605469", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759605469", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759605469#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs759605469", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759605469", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "PADIRLTFFQGDHNDGLGNA", "down_seq": "DGPGGALAHAFLPRRGEAHF", "snv": [ { "evidence": [ { "id": "rs759605469", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759605469" }, { "id": "rs759605469", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759605469#frequency_tab" }, { "id": "rs759605469", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759605469" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NAF->NAS).", "chr_id": "17", "chr_pos": "35773191", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F198", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "43", "end_pos": "52" }, { "start_pos": "91", "end_pos": "105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "58", "end_pos": "58" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H239-1.357.357", "start_pos": 357, "end_pos": 357, "uniprot_canonical_ac": "Q9H239-1", "length": 520, "uniprot_id": "MMP28_HUMAN", "protein_name": "Matrix metalloproteinase-28", "refseq_ac": "NP_001027449", "refseq_name": "matrix metalloproteinase-28 isoform 3 precursor", "gene_name": "MMP28", "gene_names_uniprotkb": "MMP28; MMP25; PRO4339", "gene_names_refseq": "EPILYSIN; MM28; MMP-25; MMP-28; MMP28", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H239", "url": "https://www.uniprot.org/uniprotkb/Q9H239" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs768108095", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768108095", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768108095", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768108095", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs768108095", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768108095#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs768108095", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768108095", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QQLYIFKGSHFWEVAADGNV", "down_seq": "EPRPLQERWVGLPPNIEAAA", "snv": [ { "evidence": [ { "id": "rs768108095", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768108095" }, { "id": "rs768108095", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768108095" }, { "id": "rs768108095", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768108095#frequency_tab" }, { "id": "rs768108095", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768108095" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVS->NVL).", "chr_id": "17", "chr_pos": "35767850", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S357", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "43", "end_pos": "52" }, { "start_pos": "91", "end_pos": "105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "58", "end_pos": "58" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q9H239-1.355.355", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H239-1.474.474", "start_pos": 474, "end_pos": 474, "uniprot_canonical_ac": "Q9H239-1", "length": 520, "uniprot_id": "MMP28_HUMAN", "protein_name": "Matrix metalloproteinase-28", "refseq_ac": "NP_001027449", "refseq_name": "matrix metalloproteinase-28 isoform 3 precursor", "gene_name": "MMP28", "gene_names_uniprotkb": "MMP28; MMP25; PRO4339", "gene_names_refseq": "EPILYSIN; MM28; MMP-25; MMP-28; MMP28", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H239", "url": "https://www.uniprot.org/uniprotkb/Q9H239" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs532783200", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs532783200", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs532783200", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs532783200", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs532783200", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs532783200", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs532783200", "url": "https://www.ncbi.nlm.nih.gov/snp/rs532783200#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs532783200", "url": "http://gnomad.broadinstitute.org/awesome?query=rs532783200", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "RSLQDWGGIPEEVSGALPRP", "down_seq": "GSIIFFRDDRYWRLDQAKLQ", "snv": [ { "evidence": [ { "id": "rs532783200", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs532783200" }, { "id": "rs532783200", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs532783200" }, { "id": "rs532783200", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs532783200" }, { "id": "rs532783200", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs532783200#frequency_tab" }, { "id": "rs532783200", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs532783200" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DGS->NGS).", "chr_id": "17", "chr_pos": "35766643", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "D474", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "43", "end_pos": "52" }, { "start_pos": "91", "end_pos": "105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "58", "end_pos": "58" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H239-1.58.58", "start_pos": 58, "end_pos": 58, "uniprot_canonical_ac": "Q9H239-1", "length": 520, "uniprot_id": "MMP28_HUMAN", "protein_name": "Matrix metalloproteinase-28", "refseq_ac": "NP_001027449", "refseq_name": "matrix metalloproteinase-28 isoform 3 precursor", "gene_name": "MMP28", "gene_names_uniprotkb": "MMP28; MMP25; PRO4339", "gene_names_refseq": "EPILYSIN; MM28; MMP-25; MMP-28; MMP28", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H239", "url": "https://www.uniprot.org/uniprotkb/Q9H239" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H239", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H239", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AFLEKYGYLNEQVPKAPTST", "down_seq": "FSDAIRAFQWVSQLPVSGVL", "snv": [ { "evidence": [ { "id": "Q9H239", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H239" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "35779263", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R58", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "43", "end_pos": "52" }, { "start_pos": "91", "end_pos": "105" } ] }, { "type": "snv", "site_list": [ { "start_pos": "130", "end_pos": "130" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "58", "end_pos": "58" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q9H239-1.43.52", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.25.25", "start_pos": 25, "end_pos": 25, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q96LW4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96LW4" }, { "database": "O-GlcNAc Atlas", "id": "Q96LW4", "url": "https://oglcnac.org/atlas/detail/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "crossref": [ { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96LW4", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96LW4", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "Q96LW4", "url": "https://oglcnac.org/atlas/detail/Q96LW4", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "WEAKLKQIEERASHYERKPL", "down_seq": "SVYRPRLSKPEEPPSIWRLF", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser25", "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q96LW4", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q96LW4" }, { "id": "Q96LW4", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q96LW4" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q96LW4-1.15.15", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96LW4-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "hPrimpol1/CCDC111 is a human DNA primase-polymerase required for the maintenance of genome integrity.", "journal": "EMBO reports", "date": "2013", "authors": "Wan L, Lou J, Xia Y, Su B, Liu T, Cui J, Sun Y, Lou H, Huang J", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "RefSeq", "id": "NP_001287696", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001287696" } ], "reference": [ { "type": "PubMed", "id": "24126761", "url": "https://glygen.org/publication/PubMed/24126761" } ] } ], "crossref": [ { "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24126761", "url": "https://glygen.org/publication/PubMed/24126761", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KNLLHCYEVIPENAVCKLYF", "down_seq": "LEFNKPANPGADGKKMVALL", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Abolishes DNA primase and polymerase activities.", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "PubMed", "id": "24126761", "url": "https://glygen.org/publication/PubMed/24126761" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q96LW4-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 0, "direction": "upstream", "id": "Q96LW4-1.114.116", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96LW4-1.114.116", "start_pos": 114, "end_pos": 116, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "PrimPol bypasses UV photoproducts during eukaryotic chromosomal DNA replication.", "journal": "Molecular cell", "date": "2013", "authors": "Bianchi J, Rudd SG, Jozwiakowski SK, Bailey LJ, Soura V, Taylor E, Stevanovic I, Green AJ, Stracker TH, Lindsay HD, Doherty AJ", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "24267451", "url": "https://glygen.org/publication/PubMed/24267451" } ] }, { "title": "PrimPol, an archaic primase/polymerase operating in human cells.", "journal": "Molecular cell", "date": "2013", "authors": "Garcia-Gomez S, Reyes A, Martinez-Jimenez MI, Chocron ES, Mouron S, Terrados G, Powell C, Salido E, Mendez J, Holt IJ, Blanco L", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "24207056", "url": "https://glygen.org/publication/PubMed/24207056" } ] }, { "title": "The Zn-finger domain of human PrimPol is required to stabilize the initiating nucleotide during DNA priming.", "journal": "Nucleic acids research", "date": "2018", "authors": "Martinez-Jimenez MI, Calvo PA, Garcia-Gomez S, Guerra-Gonzalez S, Blanco L", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "29608762", "url": "https://glygen.org/publication/PubMed/29608762" } ] }, { "title": "Molecular dissection of the domain architecture and catalytic activities of human PrimPol.", "journal": "Nucleic acids research", "date": "2014", "authors": "Keen BA, Jozwiakowski SK, Bailey LJ, Bianchi J, Doherty AJ", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "24682820", "url": "https://glygen.org/publication/PubMed/24682820" } ] }, { "title": "R-loop formation during S phase is restricted by PrimPol-mediated repriming.", "journal": "The EMBO journal", "date": "2019", "authors": "Svikovic S, Crisp A, Tan-Wong SM, Guilliam TA, Doherty AJ, Proudfoot NJ, Guilbaud G, Sale JE", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "30478192", "url": "https://glygen.org/publication/PubMed/30478192" } ] }, { "title": "PrimPol Is Required for Replicative Tolerance of G Quadruplexes in Vertebrate Cells.", "journal": "Molecular cell", "date": "2016", "authors": "Schiavone D, Jozwiakowski SK, Romanello M, Guilbaud G, Guilliam TA, Bailey LJ, Sale JE, Doherty AJ", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "RefSeq", "id": "NP_001287696", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001287696" } ], "reference": [ { "type": "PubMed", "id": "26626482", "url": "https://glygen.org/publication/PubMed/26626482" } ] }, { "title": "The invariant glutamate of human PrimPol DxE motif is critical for its Mn(2+)-dependent distinctive activities.", "journal": "DNA repair", "date": "2019", "authors": "Calvo PA, Sastre-Moreno G, Perpina C, Guerra S, Martinez-Jimenez MI, Blanco L", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "30889508", "url": "https://glygen.org/publication/PubMed/30889508" } ] } ], "crossref": [ { "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24267451", "url": "https://glygen.org/publication/PubMed/24267451", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24207056", "url": "https://glygen.org/publication/PubMed/24207056", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29608762", "url": "https://glygen.org/publication/PubMed/29608762", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24682820", "url": "https://glygen.org/publication/PubMed/24682820", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30478192", "url": "https://glygen.org/publication/PubMed/30478192", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26626482", "url": "https://glygen.org/publication/PubMed/26626482", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30889508", "url": "https://glygen.org/publication/PubMed/30889508", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "DLE", "start_aa": "D", "up_seq": "KNLLHCYEVIPENAVCKLYF", "down_seq": "FNKPANPGADGKKMVALLIE", "mutagenesis": [ { "sequence_org": "DLE", "sequence_mut": "ALA", "comment": "In AxA; abolished DNA primase and polymerase activities.", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "PubMed", "id": "24267451", "url": "https://glygen.org/publication/PubMed/24267451" }, { "database": "PubMed", "id": "24207056", "url": "https://glygen.org/publication/PubMed/24207056" }, { "database": "PubMed", "id": "29608762", "url": "https://glygen.org/publication/PubMed/29608762" }, { "database": "PubMed", "id": "24682820", "url": "https://glygen.org/publication/PubMed/24682820" }, { "database": "PubMed", "id": "30478192", "url": "https://glygen.org/publication/PubMed/30478192" }, { "database": "PubMed", "id": "26626482", "url": "https://glygen.org/publication/PubMed/26626482" }, { "database": "PubMed", "id": "30889508", "url": "https://glygen.org/publication/PubMed/30889508" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q96LW4-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 0, "direction": "downstream", "id": "Q96LW4-1.114.114", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96LW4-1.169.169", "start_pos": 169, "end_pos": 169, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "hPrimpol1/CCDC111 is a human DNA primase-polymerase required for the maintenance of genome integrity.", "journal": "EMBO reports", "date": "2013", "authors": "Wan L, Lou J, Xia Y, Su B, Liu T, Cui J, Sun Y, Lou H, Huang J", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "RefSeq", "id": "NP_001287696", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001287696" } ], "reference": [ { "type": "PubMed", "id": "24126761", "url": "https://glygen.org/publication/PubMed/24126761" } ] } ], "crossref": [ { "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24126761", "url": "https://glygen.org/publication/PubMed/24126761", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "NCSAEDVLNLDSSTDEKFSR", "down_seq": "LIFQLHDVAFKDNIHVGNFL", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "N", "comment": "Abolishes DNA primase and polymerase activities.", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "PubMed", "id": "24126761", "url": "https://glygen.org/publication/PubMed/24126761" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q96LW4-1.165.165", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96LW4-1.280.280", "start_pos": 280, "end_pos": 280, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The invariant glutamate of human PrimPol DxE motif is critical for its Mn(2+)-dependent distinctive activities.", "journal": "DNA repair", "date": "2019", "authors": "Calvo PA, Sastre-Moreno G, Perpina C, Guerra S, Martinez-Jimenez MI, Blanco L", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "30889508", "url": "https://glygen.org/publication/PubMed/30889508" } ] } ], "crossref": [ { "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30889508", "url": "https://glygen.org/publication/PubMed/30889508", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SPDLSFLVVKNNMGEKHLFV", "down_seq": "LGVYTRNRNFRLYKSSKIGK", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Abolished Mn(2+) DNA primase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "PubMed", "id": "30889508", "url": "https://glygen.org/publication/PubMed/30889508" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q96LW4-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q96LW4-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q96LW4-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q96LW4-1.294.294", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96LW4-1.419.419", "start_pos": 419, "end_pos": 419, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Molecular dissection of the domain architecture and catalytic activities of human PrimPol.", "journal": "Nucleic acids research", "date": "2014", "authors": "Keen BA, Jozwiakowski SK, Bailey LJ, Bianchi J, Doherty AJ", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "24682820", "url": "https://glygen.org/publication/PubMed/24682820" } ] }, { "title": "R-loop formation during S phase is restricted by PrimPol-mediated repriming.", "journal": "The EMBO journal", "date": "2019", "authors": "Svikovic S, Crisp A, Tan-Wong SM, Guilliam TA, Doherty AJ, Proudfoot NJ, Guilbaud G, Sale JE", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "30478192", "url": "https://glygen.org/publication/PubMed/30478192" } ] }, { "title": "PrimPol Is Required for Replicative Tolerance of G Quadruplexes in Vertebrate Cells.", "journal": "Molecular cell", "date": "2016", "authors": "Schiavone D, Jozwiakowski SK, Romanello M, Guilbaud G, Guilliam TA, Bailey LJ, Sale JE, Doherty AJ", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "RefSeq", "id": "NP_001287696", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001287696" } ], "reference": [ { "type": "PubMed", "id": "26626482", "url": "https://glygen.org/publication/PubMed/26626482" } ] }, { "title": "Repriming of DNA synthesis at stalled replication forks by human PrimPol.", "journal": "Nature structural & molecular biology", "date": "2013", "authors": "Mouron S, Rodriguez-Acebes S, Martinez-Jimenez MI, Garcia-Gomez S, Chocron S, Blanco L, Mendez J", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "24240614", "url": "https://glygen.org/publication/PubMed/24240614" } ] } ], "crossref": [ { "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24682820", "url": "https://glygen.org/publication/PubMed/24682820", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30478192", "url": "https://glygen.org/publication/PubMed/30478192", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26626482", "url": "https://glygen.org/publication/PubMed/26626482", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24240614", "url": "https://glygen.org/publication/PubMed/24240614", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "RWNYFFPEELLVYDICKYRW", "down_seq": "ENIGRAHKSNNIMILVDLKN", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "A", "comment": "Abolished zinc-binding, leading to altered translesion synthesis; when associated with A-426.", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "PubMed", "id": "24682820", "url": "https://glygen.org/publication/PubMed/24682820" }, { "database": "PubMed", "id": "30478192", "url": "https://glygen.org/publication/PubMed/30478192" }, { "database": "PubMed", "id": "26626482", "url": "https://glygen.org/publication/PubMed/26626482" } ] }, { "sequence_org": "C", "sequence_mut": "G", "comment": "In mutant CH; abolished DNA primase activity and impaired ability to restart stalled forks; when associated with Y-426.", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "PubMed", "id": "24240614", "url": "https://glygen.org/publication/PubMed/24240614" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q96LW4-1.412.412", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q96LW4-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q96LW4-1.426.426", "categories": [ "mutagenesis_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96LW4-1.426.426", "start_pos": 426, "end_pos": 426, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Molecular dissection of the domain architecture and catalytic activities of human PrimPol.", "journal": "Nucleic acids research", "date": "2014", "authors": "Keen BA, Jozwiakowski SK, Bailey LJ, Bianchi J, Doherty AJ", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "24682820", "url": "https://glygen.org/publication/PubMed/24682820" } ] }, { "title": "R-loop formation during S phase is restricted by PrimPol-mediated repriming.", "journal": "The EMBO journal", "date": "2019", "authors": "Svikovic S, Crisp A, Tan-Wong SM, Guilliam TA, Doherty AJ, Proudfoot NJ, Guilbaud G, Sale JE", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "30478192", "url": "https://glygen.org/publication/PubMed/30478192" } ] }, { "title": "PrimPol Is Required for Replicative Tolerance of G Quadruplexes in Vertebrate Cells.", "journal": "Molecular cell", "date": "2016", "authors": "Schiavone D, Jozwiakowski SK, Romanello M, Guilbaud G, Guilliam TA, Bailey LJ, Sale JE, Doherty AJ", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "RefSeq", "id": "NP_001287696", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001287696" } ], "reference": [ { "type": "PubMed", "id": "26626482", "url": "https://glygen.org/publication/PubMed/26626482" } ] }, { "title": "Repriming of DNA synthesis at stalled replication forks by human PrimPol.", "journal": "Nature structural & molecular biology", "date": "2013", "authors": "Mouron S, Rodriguez-Acebes S, Martinez-Jimenez MI, Garcia-Gomez S, Chocron S, Blanco L, Mendez J", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "24240614", "url": "https://glygen.org/publication/PubMed/24240614" } ] }, { "title": "hPrimpol1/CCDC111 is a human DNA primase-polymerase required for the maintenance of genome integrity.", "journal": "EMBO reports", "date": "2013", "authors": "Wan L, Lou J, Xia Y, Su B, Liu T, Cui J, Sun Y, Lou H, Huang J", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "RefSeq", "id": "NP_001287696", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001287696" } ], "reference": [ { "type": "PubMed", "id": "24126761", "url": "https://glygen.org/publication/PubMed/24126761" } ] } ], "crossref": [ { "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24682820", "url": "https://glygen.org/publication/PubMed/24682820", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30478192", "url": "https://glygen.org/publication/PubMed/30478192", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26626482", "url": "https://glygen.org/publication/PubMed/26626482", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24240614", "url": "https://glygen.org/publication/PubMed/24240614", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24126761", "url": "https://glygen.org/publication/PubMed/24126761", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96LW4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LW4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "EELLVYDICKYRWCENIGRA", "down_seq": "KSNNIMILVDLKNEVWYQKC", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Abolished zinc-binding, leading to altered translesion synthesis; when associated with A-419.", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "PubMed", "id": "24682820", "url": "https://glygen.org/publication/PubMed/24682820" }, { "database": "PubMed", "id": "30478192", "url": "https://glygen.org/publication/PubMed/30478192" }, { "database": "PubMed", "id": "26626482", "url": "https://glygen.org/publication/PubMed/26626482" } ] }, { "sequence_org": "H", "sequence_mut": "D", "comment": "Abolishes DNA primase activity, while it increases DNA polymerase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "PubMed", "id": "24240614", "url": "https://glygen.org/publication/PubMed/24240614" }, { "database": "PubMed", "id": "24126761", "url": "https://glygen.org/publication/PubMed/24126761" } ] }, { "sequence_org": "H", "sequence_mut": "Y", "comment": "In mutant CH; abolished DNA primase activity and impaired ability to restart stalled forks; when associated with G-419.", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "PubMed", "id": "24240614", "url": "https://glygen.org/publication/PubMed/24240614" }, { "database": "PubMed", "id": "24126761", "url": "https://glygen.org/publication/PubMed/24126761" } ] } ], "snv": [ { "evidence": [ { "id": "Q96LW4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LW4" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (HKS->NKS).", "chr_id": "4", "chr_pos": "184685665", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "H426", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q96LW4-1.412.412", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q96LW4-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q96LW4-1.419.419", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96LW4-1.519.522", "start_pos": 519, "end_pos": 522, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Molecular basis for PrimPol recruitment to replication forks by RPA.", "journal": "Nature communications", "date": "2017", "authors": "Guilliam TA, Brissett NC, Ehlinger A, Keen BA, Kolesar P, Taylor EM, Bailey LJ, Lindsay HD, Chazin WJ, Doherty AJ", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "28534480", "url": "https://glygen.org/publication/PubMed/28534480" } ] } ], "crossref": [ { "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "28534480", "url": "https://glygen.org/publication/PubMed/28534480", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "DAYF", "start_aa": "D", "up_seq": "SPSRLSTGASADAVWDNGID", "down_seq": "LEATEDAELAEAAENSLLSY", "mutagenesis": [ { "sequence_org": "DAYF", "sequence_mut": "RAYA", "comment": "Abolished interaction with RPA1, impairing recruitment to chromatin and reducing DNA primase activity; when associated with 551-R--A-554.", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "PubMed", "id": "28534480", "url": "https://glygen.org/publication/PubMed/28534480" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q96LW4-1.517.517", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96LW4-1.551.554", "start_pos": 551, "end_pos": 554, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Molecular basis for PrimPol recruitment to replication forks by RPA.", "journal": "Nature communications", "date": "2017", "authors": "Guilliam TA, Brissett NC, Ehlinger A, Keen BA, Kolesar P, Taylor EM, Bailey LJ, Lindsay HD, Chazin WJ, Doherty AJ", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "28534480", "url": "https://glygen.org/publication/PubMed/28534480" } ] } ], "crossref": [ { "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "28534480", "url": "https://glygen.org/publication/PubMed/28534480", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "DELI", "start_aa": "D", "up_seq": "LAEAAENSLLSYNSEVDEIP", "down_seq": "IEVLQE", "mutagenesis": [ { "sequence_org": "DELI", "sequence_mut": "RELA", "comment": "Abolished interaction with RPA1, impairing recruitment to chromatin and reducing DNA primase activity; when associated with 519-R--A-522.", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "PubMed", "id": "28534480", "url": "https://glygen.org/publication/PubMed/28534480" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96LW4-1.89.89", "start_pos": 89, "end_pos": 89, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Human PrimPol mutation associated with high myopia has a DNA replication defect.", "journal": "Nucleic acids research", "date": "2014", "authors": "Keen BA, Bailey LJ, Jozwiakowski SK, Doherty AJ", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "25262353", "url": "https://glygen.org/publication/PubMed/25262353" } ] } ], "crossref": [ { "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "25262353", "url": "https://glygen.org/publication/PubMed/25262353", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "CKVGDGQRIYLVTTYAEFWF", "down_seq": "YKSRKNLLHCYEVIPENAVC", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Does not affect DNA primase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "PubMed", "id": "25262353", "url": "https://glygen.org/publication/PubMed/25262353" } ] }, { "sequence_org": "Y", "sequence_mut": "S", "comment": "Reduced DNA primase activity.", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "PubMed", "id": "25262353", "url": "https://glygen.org/publication/PubMed/25262353" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q96LW4-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q96LW4-1.97.97", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q96LW4-1.15.15", "start_pos": 15, "end_pos": 15, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96LW4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LW4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MNRKWEAKLKQIEE", "down_seq": "ASHYERKPLSSVYRPRLSKP", "snv": [ { "evidence": [ { "id": "Q96LW4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LW4" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "184657183", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R15", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q96LW4-1.25.25", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.165.165", "start_pos": 165, "end_pos": 165, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753502967", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753502967", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753502967", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753502967", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753502967", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753502967#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs753502967", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753502967", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LYGVNCSAEDVLNLDSSTDE", "down_seq": "FSRHLIFQLHDVAFKDNIHV", "snv": [ { "evidence": [ { "id": "rs753502967", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753502967" }, { "id": "rs753502967", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753502967" }, { "id": "rs753502967", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753502967#frequency_tab" }, { "id": "rs753502967", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753502967" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KFS->NFS).", "chr_id": "4", "chr_pos": "184678269", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K165", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q96LW4-1.169.169", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.233.233", "start_pos": 233, "end_pos": 233, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1486465159", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1486465159", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1486465159", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1486465159", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "GHGFPHFSEAPARQGFSFNK", "down_seq": "FTEKATEESWTSNSKKLERL", "snv": [ { "evidence": [ { "id": "rs1486465159", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1486465159" }, { "id": "rs1486465159", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1486465159" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKM->NKT).", "chr_id": "4", "chr_pos": "184672314", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M233", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.262.262", "start_pos": 262, "end_pos": 262, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1756754664", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1756754664", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1756754664", "url": "https://www.ensembl.org/id/rs1756754664", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1208085599", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1208085599", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1208085599", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1208085599#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SWTSNSKKLERLGSAEQSSP", "down_seq": "LSFLVVKNNMGEKHLFVDLG", "snv": [ { "evidence": [ { "id": "rs1756754664", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1756754664" }, { "id": "rs1756754664", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1756754664" }, { "id": "rs1208085599", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1208085599" }, { "id": "rs1208085599", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1208085599#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DLS->NLS).", "chr_id": "4", "chr_pos": "184685483", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D262", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q96LW4-1.255.255", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q96LW4-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q96LW4-1.280.280", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q96LW4-1.282.282", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs374221499", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374221499", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs374221499", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374221499", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs374221499", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374221499#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs374221499", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374221499", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "RLGSAEQSSPDLSFLVVKNN", "down_seq": "GEKHLFVDLGVYTRNRNFRL", "snv": [ { "evidence": [ { "id": "rs374221499", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374221499" }, { "id": "rs374221499", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374221499" }, { "id": "rs374221499", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374221499#frequency_tab" }, { "id": "rs374221499", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374221499" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNM->NNT).", "chr_id": "4", "chr_pos": "184672431", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M272", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q96LW4-1.255.255", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q96LW4-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q96LW4-1.280.280", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q96LW4-1.282.282", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.282.282", "start_pos": 282, "end_pos": 282, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96LW4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LW4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "DLSFLVVKNNMGEKHLFVDL", "down_seq": "VYTRNRNFRLYKSSKIGKRV", "snv": [ { "evidence": [ { "id": "Q96LW4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LW4" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "184672460", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G282", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q96LW4-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q96LW4-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q96LW4-1.280.280", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q96LW4-1.294.294", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.294.294", "start_pos": 294, "end_pos": 294, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753502967", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753502967", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753502967", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753502967", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753502967", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753502967#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs753502967", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753502967", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "EKHLFVDLGVYTRNRNFRLY", "down_seq": "SSKIGKRVALEVTEDNKFFP", "snv": [ { "evidence": [ { "id": "rs753502967", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753502967" }, { "id": "rs753502967", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753502967" }, { "id": "rs753502967", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753502967#frequency_tab" }, { "id": "rs753502967", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753502967" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KSS->NSS).", "chr_id": "4", "chr_pos": "184678269", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K294", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q96LW4-1.280.280", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q96LW4-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q96LW4-1.312.312", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.312.312", "start_pos": 312, "end_pos": 312, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96LW4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LW4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "LYKSSKIGKRVALEVTEDNK", "down_seq": "FPIQSKDVSDEYQYFLSSLV", "snv": [ { "evidence": [ { "id": "Q96LW4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LW4" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "F", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NKF->NKC).", "chr_id": "4", "chr_pos": "184678322", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "F312", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q96LW4-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q96LW4-1.319.319", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.319.319", "start_pos": 319, "end_pos": 319, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs954902857", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs954902857", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs954902857", "url": "https://www.ensembl.org/id/rs954902857", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GKRVALEVTEDNKFFPIQSK", "down_seq": "VSDEYQYFLSSLVSNVRFSD", "snv": [ { "evidence": [ { "id": "rs954902857", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs954902857" }, { "id": "rs954902857", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs954902857" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DVS->NVS).", "chr_id": "4", "chr_pos": "184678342", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D319", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q96LW4-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q96LW4-1.336.336", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.336.336", "start_pos": 336, "end_pos": 336, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs538067517", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs538067517", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs538067517", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs538067517", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs538067517", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs538067517", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs538067517", "url": "https://www.ncbi.nlm.nih.gov/snp/rs538067517#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs538067517", "url": "http://gnomad.broadinstitute.org/awesome?query=rs538067517", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QSKDVSDEYQYFLSSLVSNV", "down_seq": "FSDTLRILTCEPSQNKQKGV", "snv": [ { "evidence": [ { "id": "rs538067517", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs538067517" }, { "id": "rs538067517", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs538067517" }, { "id": "rs538067517", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs538067517" }, { "id": "rs538067517", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs538067517#frequency_tab" }, { "id": "rs538067517", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs538067517" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVR->NVT).", "chr_id": "4", "chr_pos": "184678394", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R336", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q96LW4-1.319.319", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.362.362", "start_pos": 362, "end_pos": 362, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs890107889", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs890107889", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs890107889", "url": "https://www.ncbi.nlm.nih.gov/snp/rs890107889#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs890107889", "url": "http://gnomad.broadinstitute.org/awesome?query=rs890107889", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "RILTCEPSQNKQKGVGYFNS", "down_seq": "GTSVETIEGFQCSPYPEVDH", "snv": [ { "evidence": [ { "id": "rs890107889", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs890107889" }, { "id": "rs890107889", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs890107889#frequency_tab" }, { "id": "rs890107889", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs890107889" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSI->NST).", "chr_id": "4", "chr_pos": "184682325", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I362", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.412.412", "start_pos": 412, "end_pos": 412, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1756786867", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1756786867", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1756786867", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1756786867#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GIKGGIRRWNYFFPEELLVY", "down_seq": "ICKYRWCENIGRAHKSNNIM", "snv": [ { "evidence": [ { "id": "rs1756786867", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1756786867" }, { "id": "rs1756786867", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1756786867#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DIC->NIC).", "chr_id": "4", "chr_pos": "184685623", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D412", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q96LW4-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q96LW4-1.419.419", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q96LW4-1.426.426", "categories": [ "mutagenesis_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.417.417", "start_pos": 417, "end_pos": 417, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96LW4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LW4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IRRWNYFFPEELLVYDICKY", "down_seq": "WCENIGRAHKSNNIMILVDL", "snv": [ { "evidence": [ { "id": "Q96LW4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LW4" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "184685639", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R417", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "Q96LW4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LW4" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "4", "chr_pos": "184685638", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R417", "disease": [ { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q96LW4-1.412.412", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q96LW4-1.419.419", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q96LW4-1.426.426", "categories": [ "mutagenesis_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.485.485", "start_pos": 485, "end_pos": 485, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1760080874", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1760080874", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1760080874", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1760080874#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AEVCLLFLFKEEEEFTTDEA", "down_seq": "ETRSNETQNPHKPSPSRLST", "snv": [ { "evidence": [ { "id": "rs1760080874", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1760080874" }, { "id": "rs1760080874", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1760080874#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DET->NET).", "chr_id": "4", "chr_pos": "184694549", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D485", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.517.517", "start_pos": 517, "end_pos": 517, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1760111619", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1760111619", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1760111619", "url": "https://www.ensembl.org/id/rs1760111619", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "KPSPSRLSTGASADAVWDNG", "down_seq": "DDAYFLEATEDAELAEAAEN", "snv": [ { "evidence": [ { "id": "rs1760111619", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1760111619" }, { "id": "rs1760111619", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1760111619" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGI->NGT).", "chr_id": "4", "chr_pos": "184694646", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I517", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q96LW4-1.519.522", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.62.62", "start_pos": 62, "end_pos": 62, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96LW4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LW4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "WRLFHRQAQAFNFVKSCKED", "down_seq": "HVFALECKVGDGQRIYLVTT", "snv": [ { "evidence": [ { "id": "Q96LW4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LW4" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "4", "chr_pos": "184659343", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V62", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q96LW4-1.76.76", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.76.76", "start_pos": 76, "end_pos": 76, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q96LW4", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LW4", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KSCKEDVHVFALECKVGDGQ", "down_seq": "IYLVTTYAEFWFYYKSRKNL", "snv": [ { "evidence": [ { "id": "Q96LW4", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q96LW4" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "184659386", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R76", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q96LW4-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q96LW4-1.89.89", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.97.97", "start_pos": 97, "end_pos": 97, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs768524579", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768524579", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768524579", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768524579", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs768524579", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768524579", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "IYLVTTYAEFWFYYKSRKNL", "down_seq": "HCYEVIPENAVCKLYFDLEF", "snv": [ { "evidence": [ { "id": "rs768524579", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768524579" }, { "id": "rs768524579", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768524579" }, { "id": "rs768524579", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768524579" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLL->NLS).", "chr_id": "4", "chr_pos": "184661785", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L97", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q96LW4-1.89.89", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q96LW4-1.114.114", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q96LW4-1.114.116", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q96LW4-1.255.255", "start_pos": 255, "end_pos": 255, "uniprot_canonical_ac": "Q96LW4-1", "length": 560, "uniprot_id": "PRIPO_HUMAN", "protein_name": "DNA-directed primase/polymerase protein", "refseq_ac": "NP_001287696", "refseq_name": "DNA-directed primase/polymerase protein isoform 2", "gene_name": "PRIMPOL", "gene_names_uniprotkb": "PRIMPOL; CCDC111", "gene_names_refseq": "CCDC111; MYP22; PRIMPOL; Primpol1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "iPTMnet", "id": "Q96LW4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.", "journal": "Science signaling", "date": "2009", "authors": "Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "iPTMnet", "id": "Q96LW4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96LW4" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] } ], "crossref": [ { "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q96LW4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96LW4", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TEKATEESWTSNSKKLERLG", "down_seq": "AEQSSPDLSFLVVKNNMGEK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q96LW4", "url": "https://www.uniprot.org/uniprotkb/Q96LW4" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "iPTMnet", "id": "Q96LW4", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q96LW4" } ], "site_lbl": "Ser255" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "25", "end_pos": "25" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "114", "end_pos": "114" }, { "start_pos": "114", "end_pos": "116" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "519", "end_pos": "522" }, { "start_pos": "551", "end_pos": "554" }, { "start_pos": "89", "end_pos": "89" } ] }, { "type": "snv", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "412", "end_pos": "412" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "97", "end_pos": "97" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "255", "end_pos": "255" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q96LW4-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q96LW4-1.272.272", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.1020.1020", "start_pos": 1020, "end_pos": 1020, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Glycoproteomic analysis of the secretome of human endothelial cells.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Yin X, Bern M, Xing Q, Ho J, Viner R, Mayr M", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "23345538", "url": "https://glygen.org/publication/PubMed/23345538" } ] }, { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry.", "journal": "Journal of proteome research", "date": "2009", "authors": "Chen R, Jiang X, Sun D, Han G, Wang F, Ye M, Wang L, Zou H", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "reference": [ { "type": "PubMed", "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "crossref": [ { "id": "23345538", "url": "https://glygen.org/publication/PubMed/23345538", "database": "PubMed", "categories": [ "Other" ] }, { "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1275553407", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1275553407", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1275553407", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1275553407", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SQKQVKSLPKKINALKKPTV", "down_seq": "LTTVLIGRTQRNTDNIIYPE", "glycosylation": [ { "glytoucan_ac": "G00406II", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1020", "evidence": [ { "id": "23345538", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23345538" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "KPTVnLTTVLIGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1020", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G45395BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "KPTVnLTTVLIGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1020", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G57776ZS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "KPTVnLTTVLIGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1020", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G82364UA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1020", "evidence": [ { "id": "23345538", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23345538" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1020", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "19159218", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19159218" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "snv": [ { "evidence": [ { "id": "rs1275553407", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1275553407" }, { "id": "rs1275553407", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1275553407" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->KLT).", "chr_id": "4", "chr_pos": "89936740", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1020", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q13201-1.1015.1015", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13201-1.1022.1022", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q13201-1.1037.1037", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 6 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 5 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 5 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 5 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 5 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 5 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.1055.1055", "start_pos": 1055, "end_pos": 1055, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of the healthy platelet proteome identifies a new form of domain-specific O-fucosylation.", "journal": "Molecular & cellular proteomics : MCP", "date": "2024-01-16", "authors": "Houlahan Callum B, Kong Yvonne, Johnston Bede, Cielesh Michelle, Chau The Huong, Fenwick Jemma, Coleman Paul R, Hao Huilin, Haltiwanger Robert S, Thaysen-Andersen Morten, Passam Freda H, Larance Mark", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" }, { "database": "Reactome", "id": "R-HSA-5173105", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5173105" }, { "database": "Data Submission", "id": "GLY_001051", "url": "http://data.glygen.org/GLY_001051" } ], "reference": [ { "type": "PubMed", "id": "38237698", "url": "https://glygen.org/publication/PubMed/38237698" } ] }, { "title": "FUT10 and FUT11 are protein O-fucosyltransferases that modify protein EMI domains.", "journal": "Nature chemical biology", "date": "2025-01-07", "authors": "Hao Huilin, Yuan Youxi, Ito Atsuko, Eberand Benjamin M, Tjondro Harry, Cielesh Michelle, Norris Nicholas, Moreno Cesar L, Maxwell Joshua W C, Neely G Gregory, Payne Richard J, Kebede Melkam A, Urbauer Ramona J Bieber, Passam Freda H, Larance Mark, Haltiwanger Robert S", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" }, { "database": "Reactome", "id": "R-HSA-5173105", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5173105" } ], "reference": [ { "type": "PubMed", "id": "39775168", "url": "https://glygen.org/publication/PubMed/39775168" } ] } ], "crossref": [ { "id": "38237698", "url": "https://glygen.org/publication/PubMed/38237698", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_001051", "url": "http://data.glygen.org/GLY_001051", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "39775168", "url": "https://glygen.org/publication/PubMed/39775168", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs754049453", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754049453", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs754049453", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754049453", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs754049453", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754049453#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs754049453", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754049453", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs754049453", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs754049453", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NIIYPEEYSSCSRHPCQNGG", "down_seq": "CINGRTSFTCACRHPFTGDN", "glycosylation": [ { "glytoucan_ac": "G96881BQ", "type": "O-linked", "subtype": "O-fucosylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-fucosylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr1055", "evidence": [ { "id": "38237698", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38237698" }, { "id": "GLY_001051", "database": "Data Submission", "url": "http://data.glygen.org/GLY_001051" } ] }, { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-fucosylation", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (Fuc) threonine;O-fucosylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr1055", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "39775168", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39775168" }, { "id": "38237698", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38237698" } ] } ], "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "A", "comment": "Abolishes protein secretion.", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" }, { "database": "PubMed", "id": "39775168", "url": "https://glygen.org/publication/PubMed/39775168" }, { "database": "PubMed", "id": "38237698", "url": "https://glygen.org/publication/PubMed/38237698" } ] } ], "snv": [ { "evidence": [ { "id": "rs754049453", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754049453" }, { "id": "rs754049453", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754049453" }, { "id": "rs754049453", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754049453#frequency_tab" }, { "id": "rs754049453", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754049453" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->K).", "chr_id": "4", "chr_pos": "89951650", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1055", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" }, { "id": "rs754049453", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754049453" }, { "id": "rs754049453", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754049453" }, { "id": "rs754049453", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754049453#frequency_tab" }, { "id": "rs754049453", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754049453" }, { "id": "rs754049453", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs754049453" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->M).", "chr_id": "4", "chr_pos": "89951650", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T1055", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs754049453", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754049453" }, { "id": "rs754049453", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754049453" }, { "id": "rs754049453", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754049453#frequency_tab" }, { "id": "rs754049453", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754049453" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->R).", "chr_id": "4", "chr_pos": "89951650", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1055", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q13201-1.1037.1037", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q13201-1.1049.1049", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q13201-1.1058.1058", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q13201-1.1060.1060", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q13201-1.1062.1062", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q13201-1.1075.1075", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.1075.1075", "start_pos": 1075, "end_pos": 1075, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs61734879", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61734879", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs61734879", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61734879", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs61734879", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61734879", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs61734879", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61734879#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs61734879", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61734879", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TCINGRTSFTCACRHPFTGD", "down_seq": "CTIKLVEENALAPDFSKGSY", "glycosylation": [ { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HPFTGDnCTIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1075", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G57776ZS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HPFTGDnCTIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1075", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G79666IR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HPFTGDnCTIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1075", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G86880BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HPFTGDnCTIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1075", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G90659AW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HPFTGDnCTIK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1075", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1075", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" }, { "id": "rs61734879", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61734879" }, { "id": "rs61734879", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61734879" }, { "id": "rs61734879", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61734879" }, { "id": "rs61734879", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61734879#frequency_tab" }, { "id": "rs61734879", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61734879" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NCT->KCT).", "chr_id": "4", "chr_pos": "89951711", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "N1075", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q13201-1.1055.1055", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q13201-1.1058.1058", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q13201-1.1060.1060", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q13201-1.1062.1062", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13201-1.1077.1077", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 6 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 5 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 5 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 5 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 5 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 5 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry.", "journal": "Journal of proteome research", "date": "2005", "authors": "Liu T, Qian WJ, Gritsenko MA, Camp DG 2nd, Monroe ME, Moore RJ, Smith RD", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "reference": [ { "type": "PubMed", "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952" } ] }, { "title": "Elucidation of N-glycosylation sites on human platelet proteins: a glycoproteomic approach.", "journal": "Molecular & cellular proteomics : MCP", "date": "2006", "authors": "Lewandrowski U, Moebius J, Walter U, Sickmann A", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "reference": [ { "type": "PubMed", "id": "16263699", "url": "https://glygen.org/publication/PubMed/16263699" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "crossref": [ { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16263699", "url": "https://glygen.org/publication/PubMed/16263699", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1213776390", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1213776390", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1213776390", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1213776390#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1213776390", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1213776390", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs116306564", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs116306564", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs116306564", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs116306564", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs116306564", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs116306564", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs116306564", "url": "https://www.ncbi.nlm.nih.gov/snp/rs116306564#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs116306564", "url": "http://gnomad.broadinstitute.org/awesome?query=rs116306564", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GVRNQTLTSTEKAEGVVKLQ", "down_seq": "LTLPTNASIKFNPGAESVVL", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn114", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "16335952", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16335952" }, { "id": "16263699", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16263699" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "snv": [ { "evidence": [ { "id": "rs1213776390", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1213776390" }, { "id": "rs1213776390", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1213776390#frequency_tab" }, { "id": "rs1213776390", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1213776390" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->DLT).", "chr_id": "4", "chr_pos": "89895311", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N114", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs116306564", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs116306564" }, { "id": "rs116306564", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs116306564" }, { "id": "rs116306564", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs116306564" }, { "id": "rs116306564", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs116306564#frequency_tab" }, { "id": "rs116306564", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs116306564" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->ILT).", "chr_id": "4", "chr_pos": "89895312", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000784929", "site_lbl": "N114", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q13201-1.97.111", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q13201-1.97.97", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13201-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13201-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q13201-1.120.120", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q13201-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q13201-1.122.122", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.120.120", "start_pos": 120, "end_pos": 120, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry.", "journal": "Journal of proteome research", "date": "2005", "authors": "Liu T, Qian WJ, Gritsenko MA, Camp DG 2nd, Monroe ME, Moore RJ, Smith RD", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "reference": [ { "type": "PubMed", "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "crossref": [ { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs900531066", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs900531066", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs900531066", "url": "https://www.ensembl.org/id/rs900531066", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs142099842", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142099842", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs142099842", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142099842", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs142099842", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142099842", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LTSTEKAEGVVKLQNLTLPT", "down_seq": "ASIKFNPGAESVVLSNSTLK", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn120", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "16335952", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16335952" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "snv": [ { "evidence": [ { "id": "rs900531066", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs900531066" }, { "id": "rs900531066", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs900531066" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NAS->IAS).", "chr_id": "4", "chr_pos": "89895330", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N120", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs142099842", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142099842" }, { "id": "rs142099842", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142099842" }, { "id": "rs142099842", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142099842" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NAS->KAS).", "chr_id": "4", "chr_pos": "89895331", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N120", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NAS->TAS).", "chr_id": "4", "chr_pos": "89895330", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N120", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q13201-1.97.111", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q13201-1.114.114", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q13201-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q13201-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13201-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13201-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q13201-1.136.136", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q13201-1.137.137", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.136.136", "start_pos": 136, "end_pos": 136, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Distinct urinary glycoprotein signatures in prostate cancer patients.", "journal": "Oncotarget", "date": "2018", "authors": "Kawahara R, Ortega F, Rosa-Fernandes L, Guimaraes V, Quina D, Nahas W, Schwammle V, Srougi M, Leite KRM, Thaysen-Andersen M, Larsen MR, Palmisano G", "evidence": [ { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "30237853", "url": "https://glygen.org/publication/PubMed/30237853" } ] }, { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry.", "journal": "Journal of proteome research", "date": "2005", "authors": "Liu T, Qian WJ, Gritsenko MA, Camp DG 2nd, Monroe ME, Moore RJ, Smith RD", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "reference": [ { "type": "PubMed", "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952" } ] }, { "title": "A strategy for precise and large scale identification of core fucosylated glycoproteins.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Jia W, Lu Z, Fu Y, Wang HP, Wang LH, Chi H, Yuan ZF, Zheng ZB, Song LN, Han HH, Liang YM, Wang JL, Cai Y, Zhang YK, Deng YL, Ying WT, He SM, Qian XH", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "reference": [ { "type": "PubMed", "id": "19139490", "url": "https://glygen.org/publication/PubMed/19139490" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "crossref": [ { "id": "30237853", "url": "https://glygen.org/publication/PubMed/30237853", "database": "PubMed", "categories": [ "Other" ] }, { "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19139490", "url": "https://glygen.org/publication/PubMed/19139490", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs577895255", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs577895255", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs577895255", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs577895255", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs577895255", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs577895255", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs577895255", "url": "https://www.ncbi.nlm.nih.gov/snp/rs577895255#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs577895255", "url": "http://gnomad.broadinstitute.org/awesome?query=rs577895255", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TLPTNASIKFNPGAESVVLS", "down_seq": "STLKFLQSFARKSNEQATSL", "glycosylation": [ { "glytoucan_ac": "G20312EM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn136", "evidence": [ { "id": "30237853", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30237853" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FNPGAESVVLSnSTLK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn136", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G45395BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FNPGAESVVLSnSTLK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn136", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G57776ZS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FNPGAESVVLSnSTLK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn136", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G61806WR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn136", "evidence": [ { "id": "30237853", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30237853" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G70232NH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FNPGAESVVLSnSTLK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn136", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "Complex", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) (complex) asparagine;Complex", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn136", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "16335952", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16335952" }, { "id": "19139490", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19139490" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "snv": [ { "evidence": [ { "id": "rs577895255", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs577895255" }, { "id": "rs577895255", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs577895255" }, { "id": "rs577895255", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs577895255" }, { "id": "rs577895255", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs577895255#frequency_tab" }, { "id": "rs577895255", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs577895255" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NST->SST).", "chr_id": "4", "chr_pos": "89895378", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "N136", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs577895255", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs577895255" }, { "id": "rs577895255", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs577895255" }, { "id": "rs577895255", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs577895255" }, { "id": "rs577895255", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs577895255#frequency_tab" }, { "id": "rs577895255", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs577895255" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NST->TST).", "chr_id": "4", "chr_pos": "89895378", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "N136", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q13201-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q13201-1.120.120", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q13201-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q13201-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13201-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q13201-1.154.154", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 7 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 6 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 6 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 6 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 6 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 6 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.154.154", "start_pos": 154, "end_pos": 154, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "journal": "Molecular systems biology", "date": "2018", "authors": "Yang W, Ao M, Hu Y, Li QK, Zhang H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "30459171", "url": "https://glygen.org/publication/PubMed/30459171" } ] } ], "crossref": [ { "id": "30459171", "url": "https://glygen.org/publication/PubMed/30459171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LSNSTLKFLQSFARKSNEQA", "down_seq": "SLNTVGGTGGIGGVGGTGGV", "glycosylation": [ { "glytoucan_ac": "G43417UB", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr154", "evidence": [ { "id": "30459171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30459171" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q13201-1.136.136", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q13201-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q13201-1.158.158", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q13201-1.171.171", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.158.158", "start_pos": 158, "end_pos": 158, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "journal": "Molecular systems biology", "date": "2018", "authors": "Yang W, Ao M, Hu Y, Li QK, Zhang H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "30459171", "url": "https://glygen.org/publication/PubMed/30459171" } ] } ], "crossref": [ { "id": "30459171", "url": "https://glygen.org/publication/PubMed/30459171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TLKFLQSFARKSNEQATSLN", "down_seq": "VGGTGGIGGVGGTGGVGNRA", "glycosylation": [ { "glytoucan_ac": "G43417UB", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr158", "evidence": [ { "id": "30459171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30459171" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q13201-1.154.154", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q13201-1.171.171", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.171.171", "start_pos": 171, "end_pos": 171, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Studying the O-GlcNAcome of human placentas using banked tissue samples.", "journal": "Glycobiology", "date": "2024-01-22", "authors": "Luna Sarai, Malard Florian, Pereckas Michaela, Aoki Mayumi, Aoki Kazahiro, Olivier-Van Stichelen Stephanie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q13201", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13201" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13201", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs374653565", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374653565", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs374653565", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374653565", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs374653565", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374653565#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs374653565", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374653565", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EQATSLNTVGGTGGIGGVGG", "down_seq": "GGVGNRAPRETYLSRGDSSS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr171", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q13201", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13201" } ] }, { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr171", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs374653565", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374653565" }, { "id": "rs374653565", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374653565" }, { "id": "rs374653565", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374653565#frequency_tab" }, { "id": "rs374653565", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374653565" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->P).", "chr_id": "4", "chr_pos": "89895482", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T171", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q13201-1.154.154", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q13201-1.158.158", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q13201-1.190.190", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.209.209", "start_pos": 209, "end_pos": 209, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Large-scale intact glycopeptide identification by Mascot database search.", "journal": "Scientific reports", "date": "2018", "authors": "Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B", "evidence": [ { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424" } ] } ], "crossref": [ { "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424", "database": "PubMed", "categories": [ "Other" ] }, { "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "rs568621473", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs568621473", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs568621473", "url": "http://gnomad.broadinstitute.org/awesome?query=rs568621473", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SSSSQRTDYQKSNFETTRGK", "down_seq": "WCAYVHTRLSPTVILDNQVT", "glycosylation": [ { "glytoucan_ac": "G11629QQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn209", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] } ], "snv": [ { "evidence": [ { "id": "rs568621473", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs568621473" }, { "id": "rs568621473", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs568621473" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NWC->SWC).", "chr_id": "4", "chr_pos": "89909278", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N209", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q13201-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13201-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q13201-1.216.216", "categories": [ "glycosylation_flag", "mutagenesis_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.216.216", "start_pos": 216, "end_pos": 216, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of the healthy platelet proteome identifies a new form of domain-specific O-fucosylation.", "journal": "Molecular & cellular proteomics : MCP", "date": "2024-01-16", "authors": "Houlahan Callum B, Kong Yvonne, Johnston Bede, Cielesh Michelle, Chau The Huong, Fenwick Jemma, Coleman Paul R, Hao Huilin, Haltiwanger Robert S, Thaysen-Andersen Morten, Passam Freda H, Larance Mark", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" }, { "database": "Reactome", "id": "R-HSA-5173105", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5173105" }, { "database": "Data Submission", "id": "GLY_001051", "url": "http://data.glygen.org/GLY_001051" } ], "reference": [ { "type": "PubMed", "id": "38237698", "url": "https://glygen.org/publication/PubMed/38237698" } ] }, { "title": "FUT10 and FUT11 are protein O-fucosyltransferases that modify protein EMI domains.", "journal": "Nature chemical biology", "date": "2025-01-07", "authors": "Hao Huilin, Yuan Youxi, Ito Atsuko, Eberand Benjamin M, Tjondro Harry, Cielesh Michelle, Norris Nicholas, Moreno Cesar L, Maxwell Joshua W C, Neely G Gregory, Payne Richard J, Kebede Melkam A, Urbauer Ramona J Bieber, Passam Freda H, Larance Mark, Haltiwanger Robert S", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" }, { "database": "Reactome", "id": "R-HSA-5173105", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5173105" } ], "reference": [ { "type": "PubMed", "id": "39775168", "url": "https://glygen.org/publication/PubMed/39775168" } ] } ], "crossref": [ { "id": "38237698", "url": "https://glygen.org/publication/PubMed/38237698", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_001051", "url": "http://data.glygen.org/GLY_001051", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "39775168", "url": "https://glygen.org/publication/PubMed/39775168", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DYQKSNFETTRGKNWCAYVH", "down_seq": "RLSPTVILDNQVTYVPGGKG", "glycosylation": [ { "glytoucan_ac": "G96881BQ", "type": "O-linked", "subtype": "O-fucosylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-fucosylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr216", "evidence": [ { "id": "38237698", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38237698" }, { "id": "GLY_001051", "database": "Data Submission", "url": "http://data.glygen.org/GLY_001051" } ] }, { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-fucosylation", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (Fuc) threonine;O-fucosylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr216", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "39775168", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39775168" }, { "id": "38237698", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38237698" } ] } ], "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "A", "comment": "Strongly reduced protein secretion.", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" }, { "database": "PubMed", "id": "39775168", "url": "https://glygen.org/publication/PubMed/39775168" }, { "database": "PubMed", "id": "38237698", "url": "https://glygen.org/publication/PubMed/38237698" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "mutagenesis_flag" ], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q13201-1.209.209", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q13201-1.211.211", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.21.21", "start_pos": 21, "end_pos": 21, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Large-scale intact glycopeptide identification by Mascot database search.", "journal": "Scientific reports", "date": "2018", "authors": "Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B", "evidence": [ { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424" } ] }, { "title": "Glycoproteomic analysis of the secretome of human endothelial cells.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Yin X, Bern M, Xing Q, Ho J, Viner R, Mayr M", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "23345538", "url": "https://glygen.org/publication/PubMed/23345538" } ] } ], "crossref": [ { "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424", "database": "PubMed", "categories": [ "Other" ] }, { "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "23345538", "url": "https://glygen.org/publication/PubMed/23345538", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "MKGARLFVLLSSLWSGGIGL", "down_seq": "NSKHSWTIPEDGNSQKTMPS", "glycosylation": [ { "glytoucan_ac": "G37881RL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn21", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G80475RE", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn21", "evidence": [ { "id": "23345538", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23345538" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G94854LT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn21", "evidence": [ { "id": "23345538", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23345538" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn21", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q13201-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q13201-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q13201-1.28.28", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 4 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 3 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 3 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 3 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.265.265", "start_pos": 265, "end_pos": 265, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "FUT10 and FUT11 are protein O-fucosyltransferases that modify protein EMI domains.", "journal": "Nature chemical biology", "date": "2025-01-07", "authors": "Hao Huilin, Yuan Youxi, Ito Atsuko, Eberand Benjamin M, Tjondro Harry, Cielesh Michelle, Norris Nicholas, Moreno Cesar L, Maxwell Joshua W C, Neely G Gregory, Payne Richard J, Kebede Melkam A, Urbauer Ramona J Bieber, Passam Freda H, Larance Mark, Haltiwanger Robert S", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" }, { "database": "Reactome", "id": "R-HSA-5173105", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5173105" } ], "reference": [ { "type": "PubMed", "id": "39775168", "url": "https://glygen.org/publication/PubMed/39775168" } ] } ], "crossref": [ { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "39775168", "url": "https://glygen.org/publication/PubMed/39775168", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs772332445", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772332445", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772332445", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772332445", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772332445", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772332445", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1338575660", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1338575660", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1338575660", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1338575660", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "CPQRSQKISNPVYRMQHKIV", "down_seq": "SLDWRCCPGYSGPKCQLRAQ", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "O-fucosylation", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "T", "relation": "attached", "comment": "O-linked (Fuc) threonine;O-fucosylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr265", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "39775168", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39775168" } ] } ], "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "A", "comment": "Does not significantly affect protein secretion.", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" }, { "database": "PubMed", "id": "39775168", "url": "https://glygen.org/publication/PubMed/39775168" } ] } ], "snv": [ { "evidence": [ { "id": "rs772332445", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772332445" }, { "id": "rs772332445", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772332445" }, { "id": "rs772332445", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772332445" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "4", "chr_pos": "89911993", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T265", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" }, { "id": "rs1338575660", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1338575660" }, { "id": "rs1338575660", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1338575660" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->N).", "chr_id": "4", "chr_pos": "89911994", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T265", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs772332445", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772332445" }, { "id": "rs772332445", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772332445" }, { "id": "rs772332445", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772332445" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->P).", "chr_id": "4", "chr_pos": "89911993", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T265", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q13201-1.251.251", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "journal": "Molecular systems biology", "date": "2018", "authors": "Yang W, Ao M, Hu Y, Li QK, Zhang H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "30459171", "url": "https://glygen.org/publication/PubMed/30459171" } ] } ], "crossref": [ { "id": "30459171", "url": "https://glygen.org/publication/PubMed/30459171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "rs759545607", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759545607", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759545607", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759545607", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759545607", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759545607", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VLLSSLWSGGIGLNNSKHSW", "down_seq": "IPEDGNSQKTMPSASVPPNK", "glycosylation": [ { "glytoucan_ac": "G43417UB", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr28", "evidence": [ { "id": "30459171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30459171" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] } ], "snv": [ { "evidence": [ { "id": "rs759545607", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759545607" }, { "id": "rs759545607", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759545607" }, { "id": "rs759545607", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759545607" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "4", "chr_pos": "89895053", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T28", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q13201-1.21.21", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q13201-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q13201-1.24.24", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.344.344", "start_pos": 344, "end_pos": 344, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Large-scale intact glycopeptide identification by Mascot database search.", "journal": "Scientific reports", "date": "2018", "authors": "Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B", "evidence": [ { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424" } ] }, { "title": "Glycoproteomic analysis of the secretome of human endothelial cells.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Yin X, Bern M, Xing Q, Ho J, Viner R, Mayr M", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "23345538", "url": "https://glygen.org/publication/PubMed/23345538" } ] }, { "title": "Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry.", "journal": "Journal of proteome research", "date": "2009", "authors": "Chen R, Jiang X, Sun D, Han G, Wang F, Ye M, Wang L, Zou H", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "reference": [ { "type": "PubMed", "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424", "database": "PubMed", "categories": [ "Other" ] }, { "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "23345538", "url": "https://glygen.org/publication/PubMed/23345538", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "MTDQVNYQAMKLTLLQKKID", "down_seq": "ISLTVNDVRNTYSSLEGKVS", "glycosylation": [ { "glytoucan_ac": "G10819WX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "KIDnISLTVNDVR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn344", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G22310AV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn344", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "KIDnISLTVNDVR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn344", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G43089EG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn344", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G52527GH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn344", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G56784JY", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn344", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G57317CE", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn344", "evidence": [ { "id": "23345538", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23345538" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G57776ZS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "KIDnISLTVNDVR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn344", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G60145BJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn344", "evidence": [ { "id": "23345538", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23345538" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "KIDnISLTVNDVR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn344", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70441OD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "KIDnISLTVNDVR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn344", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G75983OB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn344", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G79666IR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "KIDnISLTVNDVR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn344", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "KIDnISLTVNDVR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn344", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G86880BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "KIDnISLTVNDVR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn344", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G90659AW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "KIDnISLTVNDVR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn344", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn344", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "19159218", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19159218" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q13201-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q13201-1.356.356", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 17 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 16 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 16 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 16 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 16 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 16 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.431.431", "start_pos": 431, "end_pos": 431, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Large-scale intact glycopeptide identification by Mascot database search.", "journal": "Scientific reports", "date": "2018", "authors": "Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B", "evidence": [ { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424", "database": "PubMed", "categories": [ "Other" ] }, { "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1345542786", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1345542786", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1345542786", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1345542786", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs1345542786", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1345542786", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KTVSSLSEDLESTRQIIQKV", "down_seq": "ESVVSIAAQQKFVLVQENRP", "glycosylation": [ { "glytoucan_ac": "G06247RL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VnESVVSIAAQQK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn431", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G11629QQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn431", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VnESVVSIAAQQK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn431", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G27947YN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VnESVVSIAAQQK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn431", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G40926MX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VnESVVSIAAQQK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn431", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G56784JY", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn431", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G57776ZS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VnESVVSIAAQQK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn431", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G59626AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VnESVVSIAAQQK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn431", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G60834IK", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VnESVVSIAAQQK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn431", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70441OD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VnESVVSIAAQQK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn431", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G75983OB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn431", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G79666IR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VnESVVSIAAQQK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn431", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80075MS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VnESVVSIAAQQK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn431", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G85554PZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VnESVVSIAAQQK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn431", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G86880BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VnESVVSIAAQQK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn431", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn431", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "snv": [ { "evidence": [ { "id": "rs1345542786", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1345542786" }, { "id": "rs1345542786", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1345542786" }, { "id": "rs1345542786", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1345542786" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NES->SES).", "chr_id": "4", "chr_pos": "89934972", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N431", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q13201-1.417.417", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q13201-1.421.421", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q13201-1.422.422", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13201-1.433.433", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 16 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 15 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 15 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 15 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 15 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 15 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.507.507", "start_pos": 507, "end_pos": 507, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs903267201", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs903267201", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs903267201", "url": "https://www.ncbi.nlm.nih.gov/snp/rs903267201#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs903267201", "url": "http://gnomad.broadinstitute.org/awesome?query=rs903267201", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs770854297", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770854297", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770854297", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770854297", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs770854297", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770854297#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs770854297", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770854297", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "HLEGALEQEHSRSILYYESL", "down_seq": "KTLSKLKEVHEQLLSTEQVS", "glycosylation": [ { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SILYYESLnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn507", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G79666IR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SILYYESLnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn507", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G86880BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SILYYESLnK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn507", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn507", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "snv": [ { "evidence": [ { "id": "rs903267201", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs903267201" }, { "id": "rs903267201", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs903267201#frequency_tab" }, { "id": "rs903267201", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs903267201" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKT->DKT).", "chr_id": "4", "chr_pos": "89935199", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N507", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs770854297", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770854297" }, { "id": "rs770854297", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770854297" }, { "id": "rs770854297", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770854297#frequency_tab" }, { "id": "rs770854297", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770854297" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKT->SKT).", "chr_id": "4", "chr_pos": "89935200", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N507", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs770854297", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770854297" }, { "id": "rs770854297", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770854297" }, { "id": "rs770854297", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770854297#frequency_tab" }, { "id": "rs770854297", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770854297" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKT->TKT).", "chr_id": "4", "chr_pos": "89935200", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N507", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 4 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 3 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 3 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 3 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.541.541", "start_pos": 541, "end_pos": 541, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1172420253", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1172420253", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1172420253", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1172420253", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LSTEQVSDQKNAPAAESVSN", "down_seq": "VTEYMSTLHENIKKQSLMML", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn541", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1172420253", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1172420253" }, { "id": "rs1172420253", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1172420253" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVT->TVT).", "chr_id": "4", "chr_pos": "89935302", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N541", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q13201-1.533.533", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q13201-1.555.555", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.573.573", "start_pos": 573, "end_pos": 573, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Perturbed post-translational modification (PTM) network atlas of collagen I during stent-induced neointima formation.", "journal": "Journal of proteomics", "date": "2023-02-10", "authors": "Sarohi Vivek, Basak Trayambak", "evidence": [ { "database": "GlyGen", "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481" } ], "reference": [ { "type": "PubMed", "id": "36775122", "url": "https://glygen.org/publication/PubMed/36775122" } ] } ], "crossref": [ { "id": "36775122", "url": "https://glygen.org/publication/PubMed/36775122", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000481", "url": "https://data.glygen.org/GLY_000481", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "IKKQSLMMLQMFEDLHIQES", "down_seq": "INNLTVSLEMEKESLRGECE", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "automatic_literature_mining", "site_category_dict": { "automatic_literature_mining": true }, "site_seq": "K", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Lys", "end_aa": "Lys", "residue": "Lys", "site_lbl": "Lys573", "evidence": [ { "id": "36775122", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36775122" }, { "id": "GLY_000481", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000481" } ], "mining_tool": "GlycoSiteMiner_1.0", "mining_tool_list": [ { "label": "GlycoSiteMiner_1.0" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q13201-1.555.555", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q13201-1.576.576", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q13201-1.579.579", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "mining_tool" ] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.576.576", "start_pos": 576, "end_pos": 576, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Large-scale intact glycopeptide identification by Mascot database search.", "journal": "Scientific reports", "date": "2018", "authors": "Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B", "evidence": [ { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424" } ] } ], "crossref": [ { "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424", "database": "PubMed", "categories": [ "Other" ] }, { "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1722583894", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722583894", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1722583894", "url": "https://www.ensembl.org/id/rs1722583894", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1245775900", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1245775900", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1245775900", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1245775900#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1245775900", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1245775900", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QSLMMLQMFEDLHIQESKIN", "down_seq": "LTVSLEMEKESLRGECEDML", "glycosylation": [ { "glytoucan_ac": "G11629QQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn576", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G12793SR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn576", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G39595FH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn576", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G52527GH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn576", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G57888GL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn576", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G59536GA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn576", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G62461SM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn576", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G93656SY", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn576", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn576", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1722583894", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722583894" }, { "id": "rs1722583894", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1722583894" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->DLT).", "chr_id": "4", "chr_pos": "89935406", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N576", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NLT->ILT).", "chr_id": "4", "chr_pos": "89935407", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "N576", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1245775900", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1245775900" }, { "id": "rs1245775900", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1245775900#frequency_tab" }, { "id": "rs1245775900", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1245775900" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->SLT).", "chr_id": "4", "chr_pos": "89935407", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N576", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q13201-1.573.573", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q13201-1.579.579", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 9 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 8 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 8 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 8 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 8 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 8 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.618.618", "start_pos": 618, "end_pos": 618, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Large-scale intact glycopeptide identification by Mascot database search.", "journal": "Scientific reports", "date": "2018", "authors": "Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B", "evidence": [ { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424" } ] }, { "title": "Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry.", "journal": "Journal of proteome research", "date": "2005", "authors": "Liu T, Qian WJ, Gritsenko MA, Camp DG 2nd, Monroe ME, Moore RJ, Smith RD", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "reference": [ { "type": "PubMed", "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952" } ] } ], "crossref": [ { "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424", "database": "PubMed", "categories": [ "Other" ] }, { "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs767622505", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767622505", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767622505", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767622505", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767622505", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767622505", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs750705024", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750705024", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750705024", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750705024", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750705024", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750705024", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KCRNDFKFQLKDTEENLHVL", "down_seq": "QTLAEVLFPMDNKMDKMSEQ", "glycosylation": [ { "glytoucan_ac": "G06356OH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn618", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G48414YA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn618", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn618", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "16335952", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16335952" } ] } ], "snv": [ { "evidence": [ { "id": "rs767622505", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767622505" }, { "id": "rs767622505", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767622505" }, { "id": "rs767622505", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767622505" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NQT->HQT).", "chr_id": "4", "chr_pos": "89935532", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N618", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs750705024", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750705024" }, { "id": "rs750705024", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750705024" }, { "id": "rs750705024", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750705024" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NQT->TQT).", "chr_id": "4", "chr_pos": "89935533", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N618", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q13201-1.603.603", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q13201-1.608.608", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13201-1.620.620", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q13201-1.632.632", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 3 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.680.680", "start_pos": 680, "end_pos": 680, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Large-scale intact glycopeptide identification by Mascot database search.", "journal": "Scientific reports", "date": "2018", "authors": "Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B", "evidence": [ { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424" } ] }, { "title": "Glycoproteomic analysis of the secretome of human endothelial cells.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Yin X, Bern M, Xing Q, Ho J, Viner R, Mayr M", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "23345538", "url": "https://glygen.org/publication/PubMed/23345538" } ] } ], "crossref": [ { "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424", "database": "PubMed", "categories": [ "Other" ] }, { "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "23345538", "url": "https://glygen.org/publication/PubMed/23345538", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs763943890", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763943890", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763943890", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763943890", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763943890", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763943890", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RQTMTYEQPKEAIVIRKKIE", "down_seq": "LTSAVNSLNFIIKELTKRHN", "glycosylation": [ { "glytoucan_ac": "G10019LZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn680", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G14669DU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn680", "evidence": [ { "id": "23345538", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23345538" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G28681TP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn680", "evidence": [ { "id": "23345538", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23345538" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G62461SM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn680", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn680", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs763943890", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763943890" }, { "id": "rs763943890", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763943890" }, { "id": "rs763943890", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763943890" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->SLT).", "chr_id": "4", "chr_pos": "89935719", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N680", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NLT->YLT).", "chr_id": "4", "chr_pos": "89935718", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "N680", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 5 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 4 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 4 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 4 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 4 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 4 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.729.729", "start_pos": 729, "end_pos": 729, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry.", "journal": "Journal of proteome research", "date": "2009", "authors": "Chen R, Jiang X, Sun D, Han G, Wang F, Ye M, Wang L, Zou H", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "reference": [ { "type": "PubMed", "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218" } ] }, { "title": "Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry.", "journal": "Journal of proteome research", "date": "2005", "authors": "Liu T, Qian WJ, Gritsenko MA, Camp DG 2nd, Monroe ME, Moore RJ, Smith RD", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "reference": [ { "type": "PubMed", "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952" } ] } ], "crossref": [ { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1374823060", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1374823060", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1374823060", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1374823060#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RDDALERRINEYALEMEDGL", "down_seq": "KTMTIINNAIDFIQDNYALK", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn729", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "19159218", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19159218" }, { "id": "16335952", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16335952" } ] } ], "snv": [ { "evidence": [ { "id": "rs1374823060", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1374823060" }, { "id": "rs1374823060", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1374823060#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKT->DKT).", "chr_id": "4", "chr_pos": "89935865", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N729", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NKT->SKT).", "chr_id": "4", "chr_pos": "89935866", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N729", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q13201-1.720.720", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13201-1.731.731", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q13201-1.732.732", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q13201-1.738.738", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q13201-1.739.739", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q13201-1.747.747", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.73.73", "start_pos": 73, "end_pos": 73, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mapping the O-glycoproteome using site-specific extraction of O-linked glycopeptides (EXoO).", "journal": "Molecular systems biology", "date": "2018", "authors": "Yang W, Ao M, Hu Y, Li QK, Zhang H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "30459171", "url": "https://glygen.org/publication/PubMed/30459171" } ] } ], "crossref": [ { "id": "30459171", "url": "https://glygen.org/publication/PubMed/30459171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "rs753383506", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753383506", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753383506", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753383506", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753383506", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753383506", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs753383506", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs753383506", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QILPTTRVMSAEIATTPEAR", "down_seq": "SEDSLLKSTLPPSETSAPAE", "glycosylation": [ { "glytoucan_ac": "G43417UB", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr73", "evidence": [ { "id": "30459171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30459171" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] } ], "snv": [ { "evidence": [ { "id": "rs753383506", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753383506" }, { "id": "rs753383506", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753383506" }, { "id": "rs753383506", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753383506" }, { "id": "rs753383506", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs753383506" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->N).", "chr_id": "4", "chr_pos": "89895189", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T73", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q13201-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q13201-1.80.80", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.783.783", "start_pos": 783, "end_pos": 783, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Large-scale intact glycopeptide identification by Mascot database search.", "journal": "Scientific reports", "date": "2018", "authors": "Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B", "evidence": [ { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424", "database": "PubMed", "categories": [ "Other" ] }, { "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1201447240", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1201447240", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1201447240", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1201447240#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1201447240", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1201447240", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "HKCTSDMETILTFIPQFHRL", "down_seq": "DSIQTLVNDNQRYNFVLQVA", "glycosylation": [ { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LnDSIQTLVNDNQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn783", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G48414YA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn783", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G57776ZS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LnDSIQTLVNDNQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn783", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G64394MX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn783", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G79666IR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LnDSIQTLVNDNQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn783", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80075MS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LnDSIQTLVNDNQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn783", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn783", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "snv": [ { "evidence": [ { "id": "rs1201447240", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1201447240" }, { "id": "rs1201447240", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1201447240#frequency_tab" }, { "id": "rs1201447240", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1201447240" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NDS->SDS).", "chr_id": "4", "chr_pos": "89936028", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N783", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q13201-1.768.768", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13201-1.785.785", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q13201-1.793.793", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q13201-1.794.794", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q13201-1.795.795", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 7 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 6 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 6 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 6 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 6 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 6 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.816.816", "start_pos": 816, "end_pos": 816, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Large-scale intact glycopeptide identification by Mascot database search.", "journal": "Scientific reports", "date": "2018", "authors": "Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B", "evidence": [ { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424" } ] }, { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "crossref": [ { "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424", "database": "PubMed", "categories": [ "Other" ] }, { "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "YNFVLQVAKTLAGIPRDEKL", "down_seq": "QSNFQKMYQMFNETTSQVRK", "glycosylation": [ { "glytoucan_ac": "G11629QQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn816", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LnQSNFQK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn816", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G56784JY", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn816", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G57776ZS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LnQSNFQK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn816", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70232NH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LnQSNFQK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn816", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70441OD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LnQSNFQK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn816", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G86880BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LnQSNFQK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn816", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn816", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q13201-1.818.818", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q13201-1.828.828", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q13201-1.830.830", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 8 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 7 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 7 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 7 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 7 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 7 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.828.828", "start_pos": 828, "end_pos": 828, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Glycoproteomic analysis of the secretome of human endothelial cells.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Yin X, Bern M, Xing Q, Ho J, Viner R, Mayr M", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "23345538", "url": "https://glygen.org/publication/PubMed/23345538" } ] }, { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Site-Specific Profiling of Serum Glycoproteins Using N-Linked Glycan and Glycosite Analysis Revealing Atypical N-Glycosylation Sites on Albumin and alpha-1B-Glycoprotein.", "journal": "Analytical chemistry", "date": "2018", "authors": "Sun S, Hu Y, Jia L, Eshghi ST, Liu Y, Shah P, Zhang H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "29671580", "url": "https://glygen.org/publication/PubMed/29671580" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "crossref": [ { "id": "23345538", "url": "https://glygen.org/publication/PubMed/23345538", "database": "PubMed", "categories": [ "Other" ] }, { "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29671580", "url": "https://glygen.org/publication/PubMed/29671580", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1187501533", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1187501533", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1187501533", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1187501533#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1187501533", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1187501533", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GIPRDEKLNQSNFQKMYQMF", "down_seq": "ETTSQVRKYQQNMSHLEEKL", "glycosylation": [ { "glytoucan_ac": "G02030ZB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn828", "evidence": [ { "id": "23345538", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23345538" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G12580WI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn828", "evidence": [ { "id": "23345538", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23345538" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "MYQMFnETTSQVR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn828", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G54992WG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn828", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G83676GD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn828", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn828", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "snv": [ { "evidence": [ { "id": "rs1187501533", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1187501533" }, { "id": "rs1187501533", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1187501533#frequency_tab" }, { "id": "rs1187501533", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1187501533" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NET->HET).", "chr_id": "4", "chr_pos": "89936162", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N828", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q13201-1.816.816", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q13201-1.818.818", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13201-1.830.830", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q13201-1.840.840", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q13201-1.842.842", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 6 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 5 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 5 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 5 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 5 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 5 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.840.840", "start_pos": 840, "end_pos": 840, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Large-scale intact glycopeptide identification by Mascot database search.", "journal": "Scientific reports", "date": "2018", "authors": "Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B", "evidence": [ { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424", "database": "PubMed", "categories": [ "Other" ] }, { "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1244428335", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1244428335", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1244428335", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1244428335#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FQKMYQMFNETTSQVRKYQQ", "down_seq": "MSHLEEKLLLTTKISKNFET", "glycosylation": [ { "glytoucan_ac": "G01650EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G02815KT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G04657PL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G10486CT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G18647XP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G28541PG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G37399XV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G39446WN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G47644PP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G56784JY", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G57776ZS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G58954YZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G59626AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G63041LO", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70619PT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G90659AW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G92050GC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "YQQnMSHLEEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn840", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "snv": [ { "evidence": [ { "id": "rs1244428335", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1244428335" }, { "id": "rs1244428335", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1244428335#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NMS->IMS).", "chr_id": "4", "chr_pos": "89936199", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N840", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q13201-1.828.828", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q13201-1.830.830", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13201-1.842.842", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 21 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 20 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 20 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 20 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 20 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 20 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.921.921", "start_pos": 921, "end_pos": 921, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Glycoproteomic analysis of the secretome of human endothelial cells.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Yin X, Bern M, Xing Q, Ho J, Viner R, Mayr M", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "23345538", "url": "https://glygen.org/publication/PubMed/23345538" } ] } ], "crossref": [ { "id": "23345538", "url": "https://glygen.org/publication/PubMed/23345538", "database": "PubMed", "categories": [ "Other" ] }, { "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SRFKALEAKSIHLSINFFSL", "down_seq": "KTLHEVLTMCHNASTSVSEL", "glycosylation": [ { "glytoucan_ac": "G14669DU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn921", "evidence": [ { "id": "23345538", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23345538" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G28681TP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn921", "evidence": [ { "id": "23345538", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23345538" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn921", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NKT->SKT).", "chr_id": "4", "chr_pos": "89936442", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N921", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q13201-1.917.917", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13201-1.923.923", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q13201-1.926.926", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q13201-1.933.933", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q13201-1.934.934", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q13201-1.935.935", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 3 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.933.933", "start_pos": 933, "end_pos": 933, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs753993168", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753993168", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753993168", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753993168", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753993168", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753993168#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs753993168", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753993168", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LSINFFSLNKTLHEVLTMCH", "down_seq": "ASTSVSELNATIPKWIKHSL", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn933", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs753993168", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753993168" }, { "id": "rs753993168", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753993168" }, { "id": "rs753993168", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753993168#frequency_tab" }, { "id": "rs753993168", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753993168" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NAS->IAS).", "chr_id": "4", "chr_pos": "89936478", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N933", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs753993168", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753993168" }, { "id": "rs753993168", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753993168" }, { "id": "rs753993168", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753993168#frequency_tab" }, { "id": "rs753993168", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753993168" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NAS->SAS).", "chr_id": "4", "chr_pos": "89936478", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N933", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q13201-1.917.917", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q13201-1.921.921", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q13201-1.923.923", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q13201-1.926.926", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13201-1.934.934", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13201-1.935.935", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q13201-1.942.942", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.942.942", "start_pos": 942, "end_pos": 942, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry.", "journal": "Journal of proteome research", "date": "2009", "authors": "Chen R, Jiang X, Sun D, Han G, Wang F, Ye M, Wang L, Zou H", "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "reference": [ { "type": "PubMed", "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218" } ] } ], "crossref": [ { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1264182143", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1264182143", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1264182143", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1264182143#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1722644963", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722644963", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1722644963", "url": "https://www.ensembl.org/id/rs1722644963", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KTLHEVLTMCHNASTSVSEL", "down_seq": "ATIPKWIKHSLPDIQLLQKG", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn942", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "19159218", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19159218" } ] } ], "snv": [ { "evidence": [ { "id": "rs1264182143", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1264182143" }, { "id": "rs1264182143", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1264182143#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NAT->DAT).", "chr_id": "4", "chr_pos": "89936504", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N942", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1722644963", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722644963" }, { "id": "rs1722644963", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1722644963" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NAT->SAT).", "chr_id": "4", "chr_pos": "89936505", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N942", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q13201-1.923.923", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q13201-1.926.926", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q13201-1.933.933", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q13201-1.934.934", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q13201-1.935.935", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.97.111", "start_pos": 97, "end_pos": 111, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Proteomics Analysis of O-GalNAc Glycosylation in Human Serum by an Integrated Strategy.", "journal": "Analytical chemistry", "date": "2017", "authors": "Qin H, Cheng K, Zhu J, Mao J, Wang F, Dong M, Chen R, Guo Z, Liang X, Ye M, Zou H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "28035807", "url": "https://glygen.org/publication/PubMed/28035807" } ] }, { "title": "Proteomics Analysis of O-GalNAc Glycosylation in Human Serum by an Integrated Strategy", "journal": "Anal. Chem.", "date": "2017", "authors": "Qin H., Cheng K., Zhu J., Mao J., Wang F., Dong M., Chen R., Guo Z., Liang X., Ye M., Zou H.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1021/acs.analchem.6b02887", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.6b02887" } ] } ], "crossref": [ { "id": "28035807", "url": "https://glygen.org/publication/PubMed/28035807", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "10.1021/acs.analchem.6b02887", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.6b02887", "database": "DOI", "categories": [ "Other" ] } ], "site_seq": "NQTLTSTEKAEGVVK", "start_aa": "N", "up_seq": "SLLKSTLPPSETSAPAEGVR", "down_seq": "LQNLTLPTNASIKFNPGAES", "glycosylation": [ { "glytoucan_ac": "G57321FI", "type": "O-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NQTLTSTEKAEGVVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Lys", "evidence": [ { "id": "28035807", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28035807" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1021/acs.analchem.6b02887", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1021/acs.analchem.6b02887" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q13201-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q13201-1.97.97", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q13201-1.114.114", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q13201-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q13201-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q13201-1.120.120", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q13201-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q13201-1.122.122", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.97.97", "start_pos": 97, "end_pos": 97, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Large-scale intact glycopeptide identification by Mascot database search.", "journal": "Scientific reports", "date": "2018", "authors": "Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B", "evidence": [ { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424" } ] }, { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] } ], "crossref": [ { "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424", "database": "PubMed", "categories": [ "Other" ] }, { "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs771864874", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771864874", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771864874", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771864874", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771864874", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771864874", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SLLKSTLPPSETSAPAEGVR", "down_seq": "QTLTSTEKAEGVVKLQNLTL", "glycosylation": [ { "glytoucan_ac": "G34617SM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn97", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G37881RL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn97", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nQTLTSTEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn97", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn97", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs771864874", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771864874" }, { "id": "rs771864874", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771864874" }, { "id": "rs771864874", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771864874" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NQT->IQT).", "chr_id": "4", "chr_pos": "89895261", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N97", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q13201-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q13201-1.97.111", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q13201-1.114.114", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q13201-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q13201-1.116.116", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 4 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 3 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 3 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 3 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.981.981", "start_pos": 981, "end_pos": 981, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Large-scale intact glycopeptide identification by Mascot database search.", "journal": "Scientific reports", "date": "2018", "authors": "Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B", "evidence": [ { "database": "GlyConnect", "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ], "reference": [ { "type": "PubMed", "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424" } ] }, { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "crossref": [ { "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424", "database": "PubMed", "categories": [ "Other" ] }, { "id": "668", "url": "https://glyconnect.expasy.org/browser/proteins/668", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KGLTEFVEPIIQIKTQAALS", "down_seq": "LTCCIDRSLPGSLANVVKSQ", "glycosylation": [ { "glytoucan_ac": "G34617SM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn981", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "G57776ZS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "TQAALSnLTCCIDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn981", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G64394MX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn981", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "668", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/668" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn981", "evidence": [ { "id": "Q13201", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q13201#ptm_processing" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q13201-1.983.983", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q13201-1.987.987", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 4 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 3 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 3 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 3 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.1015.1015", "start_pos": 1015, "end_pos": 1015, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ANVVKSQKQVKSLPKKINAL", "down_seq": "KPTVNLTTVLIGRTQRNTDN", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "89936725", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K1015", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q13201-1.1020.1020", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q13201-1.1022.1022", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.1022.1022", "start_pos": 1022, "end_pos": 1022, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KQVKSLPKKINALKKPTVNL", "down_seq": "TVLIGRTQRNTDNIIYPEEY", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NLT->NLN).", "chr_id": "4", "chr_pos": "89936745", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T1022", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q13201-1.1015.1015", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13201-1.1020.1020", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q13201-1.1037.1037", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.1037.1037", "start_pos": 1037, "end_pos": 1037, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs535383970", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs535383970", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs535383970", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs535383970", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs535383970", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs535383970", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs535383970", "url": "https://www.ncbi.nlm.nih.gov/snp/rs535383970#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs535383970", "url": "http://gnomad.broadinstitute.org/awesome?query=rs535383970", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "PTVNLTTVLIGRTQRNTDNI", "down_seq": "YPEEYSSCSRHPCQNGGTCI", "snv": [ { "evidence": [ { "id": "rs535383970", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs535383970" }, { "id": "rs535383970", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs535383970" }, { "id": "rs535383970", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs535383970" }, { "id": "rs535383970", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs535383970#frequency_tab" }, { "id": "rs535383970", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs535383970" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NII->NIT).", "chr_id": "4", "chr_pos": "89936790", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "I1037", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q13201-1.1020.1020", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q13201-1.1022.1022", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q13201-1.1049.1049", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q13201-1.1055.1055", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.1049.1049", "start_pos": 1049, "end_pos": 1049, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "TQRNTDNIIYPEEYSSCSRH", "down_seq": "CQNGGTCINGRTSFTCACRH", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "4", "chr_pos": "89951632", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P1049", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q13201-1.1037.1037", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q13201-1.1055.1055", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q13201-1.1058.1058", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q13201-1.1060.1060", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q13201-1.1062.1062", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.1058.1058", "start_pos": 1058, "end_pos": 1058, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "YPEEYSSCSRHPCQNGGTCI", "down_seq": "GRTSFTCACRHPFTGDNCTI", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "89951658", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N1058", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q13201-1.1049.1049", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q13201-1.1055.1055", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13201-1.1060.1060", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q13201-1.1062.1062", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q13201-1.1075.1075", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q13201-1.1077.1077", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.1060.1060", "start_pos": 1060, "end_pos": 1060, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1560601575", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1560601575", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1560601575", "url": "https://www.ensembl.org/id/rs1560601575", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EEYSSCSRHPCQNGGTCING", "down_seq": "TSFTCACRHPFTGDNCTIKL", "snv": [ { "evidence": [ { "id": "rs1560601575", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1560601575" }, { "id": "rs1560601575", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1560601575" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGR->NGT).", "chr_id": "4", "chr_pos": "89951665", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1060", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q13201-1.1049.1049", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q13201-1.1055.1055", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13201-1.1058.1058", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13201-1.1062.1062", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q13201-1.1075.1075", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q13201-1.1077.1077", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.1062.1062", "start_pos": 1062, "end_pos": 1062, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs776315168", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776315168", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776315168", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776315168", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776315168", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776315168", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YSSCSRHPCQNGGTCINGRT", "down_seq": "FTCACRHPFTGDNCTIKLVE", "snv": [ { "evidence": [ { "id": "rs776315168", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776315168" }, { "id": "rs776315168", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776315168" }, { "id": "rs776315168", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776315168" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SFT->NFT).", "chr_id": "4", "chr_pos": "89951671", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1062", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q13201-1.1049.1049", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q13201-1.1055.1055", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q13201-1.1058.1058", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13201-1.1060.1060", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q13201-1.1075.1075", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q13201-1.1077.1077", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.1077.1077", "start_pos": 1077, "end_pos": 1077, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs577344792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs577344792", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs577344792", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs577344792", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs577344792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs577344792", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs577344792", "url": "http://gnomad.broadinstitute.org/awesome?query=rs577344792", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "INGRTSFTCACRHPFTGDNC", "down_seq": "IKLVEENALAPDFSKGSYRY", "snv": [ { "evidence": [ { "id": "rs577344792", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs577344792" }, { "id": "rs577344792", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs577344792" }, { "id": "rs577344792", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs577344792" }, { "id": "rs577344792", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs577344792" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NCT->NCA).", "chr_id": "4", "chr_pos": "89951715", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "T1077", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NCT->NCI).", "chr_id": "4", "chr_pos": "89951716", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T1077", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q13201-1.1058.1058", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q13201-1.1060.1060", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q13201-1.1062.1062", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13201-1.1075.1075", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.1108.1108", "start_pos": 1108, "end_pos": 1108, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PDFSKGSYRYAPMVAFFASH", "down_seq": "YGMTIPGPILFNNLDVNYGA", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "4", "chr_pos": "89953054", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T1108", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q13201-1.1122.1122", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.1122.1122", "start_pos": 1122, "end_pos": 1122, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "AFFASHTYGMTIPGPILFNN", "down_seq": "DVNYGASYTPRTGKFRIPYL", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NNL->NNS).", "chr_id": "4", "chr_pos": "89953096", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "L1122", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q13201-1.1108.1108", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.1148.1148", "start_pos": 1148, "end_pos": 1148, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1578510248", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1578510248", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1578510248", "url": "https://www.ensembl.org/id/rs1578510248", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1578510248", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1578510248", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ASYTPRTGKFRIPYLGVYVF", "down_seq": "YTIESFSAHISGFLVVDGID", "snv": [ { "evidence": [ { "id": "rs1578510248", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1578510248" }, { "id": "rs1578510248", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1578510248" }, { "id": "rs1578510248", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1578510248" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KYT->NYT).", "chr_id": "4", "chr_pos": "89953175", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1148", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q13201-1.1151.1151", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q13201-1.1152.1152", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.1151.1151", "start_pos": 1151, "end_pos": 1151, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs138433713", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138433713", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs138433713", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138433713", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs138433713", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138433713", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "TPRTGKFRIPYLGVYVFKYT", "down_seq": "ESFSAHISGFLVVDGIDKLA", "snv": [ { "evidence": [ { "id": "rs138433713", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138433713" }, { "id": "rs138433713", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138433713" }, { "id": "rs138433713", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138433713" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IES->NES).", "chr_id": "4", "chr_pos": "89953183", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1151", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q13201-1.1148.1148", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13201-1.1152.1152", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.1152.1152", "start_pos": 1152, "end_pos": 1152, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "PRTGKFRIPYLGVYVFKYTI", "down_seq": "SFSAHISGFLVVDGIDKLAF", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "89953185", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E1152", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q13201-1.1148.1148", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13201-1.1151.1151", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.115.115", "start_pos": 115, "end_pos": 115, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs750773945", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750773945", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750773945", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750773945", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750773945", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750773945#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs750773945", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750773945", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "VRNQTLTSTEKAEGVVKLQN", "down_seq": "TLPTNASIKFNPGAESVVLS", "snv": [ { "evidence": [ { "id": "rs750773945", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750773945" }, { "id": "rs750773945", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750773945" }, { "id": "rs750773945", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750773945#frequency_tab" }, { "id": "rs750773945", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750773945" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->NPT).", "chr_id": "4", "chr_pos": "89895315", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L115", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q13201-1.97.111", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q13201-1.97.97", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13201-1.114.114", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13201-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q13201-1.120.120", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q13201-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q13201-1.122.122", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.116.116", "start_pos": 116, "end_pos": 116, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs756540121", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756540121", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756540121", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756540121", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756540121", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756540121", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs756540121", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs756540121", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RNQTLTSTEKAEGVVKLQNL", "down_seq": "LPTNASIKFNPGAESVVLSN", "snv": [ { "evidence": [ { "id": "rs756540121", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756540121" }, { "id": "rs756540121", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756540121" }, { "id": "rs756540121", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756540121" }, { "id": "rs756540121", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs756540121" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NLT->NLI).", "chr_id": "4", "chr_pos": "89895318", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T116", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs756540121", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756540121" }, { "id": "rs756540121", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756540121" }, { "id": "rs756540121", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756540121" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->NLN).", "chr_id": "4", "chr_pos": "89895318", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T116", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q13201-1.97.111", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q13201-1.97.97", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13201-1.114.114", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13201-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q13201-1.120.120", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q13201-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q13201-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q13201-1.136.136", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.1177.1177", "start_pos": 1177, "end_pos": 1177, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1299258340", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1299258340", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1299258340", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1299258340#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1299258340", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1299258340", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "HISGFLVVDGIDKLAFESEN", "down_seq": "NSEIHCDRVLTGDALLELNY", "snv": [ { "evidence": [ { "id": "rs1299258340", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1299258340" }, { "id": "rs1299258340", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1299258340#frequency_tab" }, { "id": "rs1299258340", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1299258340" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (INS->NNS).", "chr_id": "4", "chr_pos": "89953261", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1177", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.121.121", "start_pos": 121, "end_pos": 121, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1047372866", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1047372866", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1047372866", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1047372866#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1047372866", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1047372866", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TSTEKAEGVVKLQNLTLPTN", "down_seq": "SIKFNPGAESVVLSNSTLKF", "snv": [ { "evidence": [ { "id": "rs1047372866", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1047372866" }, { "id": "rs1047372866", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1047372866#frequency_tab" }, { "id": "rs1047372866", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1047372866" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NAS->NPS).", "chr_id": "4", "chr_pos": "89895332", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A121", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q13201-1.97.111", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q13201-1.114.114", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q13201-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q13201-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13201-1.120.120", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13201-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q13201-1.136.136", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q13201-1.137.137", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.122.122", "start_pos": 122, "end_pos": 122, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs748302988", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748302988", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748302988", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748302988", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748302988", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748302988", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1283065784", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1283065784", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1283065784", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1283065784", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STEKAEGVVKLQNLTLPTNA", "down_seq": "IKFNPGAESVVLSNSTLKFL", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NAS->NAG).", "chr_id": "4", "chr_pos": "89895335", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S122", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs748302988", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748302988" }, { "id": "rs748302988", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748302988" }, { "id": "rs748302988", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748302988" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NAS->NAN).", "chr_id": "4", "chr_pos": "89895336", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S122", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" }, { "id": "rs1283065784", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1283065784" }, { "id": "rs1283065784", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1283065784" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NAS->NAR).", "chr_id": "4", "chr_pos": "89895337", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S122", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q13201-1.97.111", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q13201-1.114.114", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q13201-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q13201-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13201-1.120.120", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13201-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q13201-1.136.136", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q13201-1.137.137", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.137.137", "start_pos": 137, "end_pos": 137, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs371738397", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371738397", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371738397", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371738397", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs371738397", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371738397#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs371738397", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371738397", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LPTNASIKFNPGAESVVLSN", "down_seq": "TLKFLQSFARKSNEQATSLN", "snv": [ { "evidence": [ { "id": "rs371738397", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371738397" }, { "id": "rs371738397", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371738397" }, { "id": "rs371738397", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371738397#frequency_tab" }, { "id": "rs371738397", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371738397" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NST->NPT).", "chr_id": "4", "chr_pos": "89895380", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S137", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q13201-1.120.120", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q13201-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q13201-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13201-1.136.136", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q13201-1.154.154", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.190.190", "start_pos": 190, "end_pos": 190, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs781247540", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781247540", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781247540", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781247540", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781247540", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781247540", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GTGGVGNRAPRETYLSRGDS", "down_seq": "SSQRTDYQKSNFETTRGKNW", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" }, { "id": "rs781247540", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781247540" }, { "id": "rs781247540", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781247540" }, { "id": "rs781247540", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781247540" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SSS->NSS).", "chr_id": "4", "chr_pos": "89895540", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S190", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q13201-1.171.171", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q13201-1.209.209", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.211.211", "start_pos": 211, "end_pos": 211, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1721666045", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1721666045", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1721666045", "url": "https://www.ensembl.org/id/rs1721666045", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs376506594", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376506594", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs376506594", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376506594", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs376506594", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376506594#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs376506594", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376506594", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "SSQRTDYQKSNFETTRGKNW", "down_seq": "AYVHTRLSPTVILDNQVTYV", "snv": [ { "evidence": [ { "id": "rs1721666045", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1721666045" }, { "id": "rs1721666045", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1721666045" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "C", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NWC->NW*).", "chr_id": "4", "chr_pos": "89909285", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C211", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs376506594", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376506594" }, { "id": "rs376506594", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376506594" }, { "id": "rs376506594", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376506594#frequency_tab" }, { "id": "rs376506594", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376506594" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "C", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NWC->NWY).", "chr_id": "4", "chr_pos": "89909284", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C211", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q13201-1.209.209", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q13201-1.216.216", "categories": [ "glycosylation_flag", "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.23.23", "start_pos": 23, "end_pos": 23, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs747379966", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747379966", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747379966", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747379966", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747379966", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747379966#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs747379966", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747379966", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GARLFVLLSSLWSGGIGLNN", "down_seq": "KHSWTIPEDGNSQKTMPSAS", "snv": [ { "evidence": [ { "id": "rs747379966", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747379966" }, { "id": "rs747379966", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747379966" }, { "id": "rs747379966", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747379966#frequency_tab" }, { "id": "rs747379966", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747379966" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NNS->NNN).", "chr_id": "4", "chr_pos": "89895039", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S23", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q13201-1.21.21", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13201-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q13201-1.28.28", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.24.24", "start_pos": 24, "end_pos": 24, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs550198498", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs550198498", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs550198498", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs550198498", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs550198498", "url": "https://www.ncbi.nlm.nih.gov/snp/rs550198498#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs550198498", "url": "http://gnomad.broadinstitute.org/awesome?query=rs550198498", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ARLFVLLSSLWSGGIGLNNS", "down_seq": "HSWTIPEDGNSQKTMPSASV", "snv": [ { "evidence": [ { "id": "rs550198498", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs550198498" }, { "id": "rs550198498", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs550198498" }, { "id": "rs550198498", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs550198498#frequency_tab" }, { "id": "rs550198498", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs550198498" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KHS->NHS).", "chr_id": "4", "chr_pos": "89895043", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K24", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q13201-1.21.21", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13201-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q13201-1.28.28", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.251.251", "start_pos": 251, "end_pos": 251, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs765205422", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765205422", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765205422", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765205422", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765205422", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765205422", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VPGGKGPCGWTGGSCPQRSQ", "down_seq": "ISNPVYRMQHKIVTSLDWRC", "snv": [ { "evidence": [ { "id": "rs765205422", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765205422" }, { "id": "rs765205422", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765205422" }, { "id": "rs765205422", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765205422" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KIS->NIS).", "chr_id": "4", "chr_pos": "89911953", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K251", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q13201-1.265.265", "categories": [ "glycosylation_flag", "mutagenesis_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.296.296", "start_pos": 296, "end_pos": 296, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SGPKCQLRAQEQQSLIHTNQ", "down_seq": "ESHTAVGRGVAEQQQQQGCG", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NQA->NQS).", "chr_id": "4", "chr_pos": "89923203", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A296", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.346.346", "start_pos": 346, "end_pos": 346, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DQVNYQAMKLTLLQKKIDNI", "down_seq": "LTVNDVRNTYSSLEGKVSED", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NIS->NIF).", "chr_id": "4", "chr_pos": "89927876", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S346", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "S", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NIS->NIY).", "chr_id": "4", "chr_pos": "89927876", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S346", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q13201-1.344.344", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q13201-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q13201-1.366.366", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.356.356", "start_pos": 356, "end_pos": 356, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1722313255", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722313255", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1722313255", "url": "https://www.ensembl.org/id/rs1722313255", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "TLLQKKIDNISLTVNDVRNT", "down_seq": "SSLEGKVSEDKSREFQSLLK", "snv": [ { "evidence": [ { "id": "rs1722313255", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722313255" }, { "id": "rs1722313255", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1722313255" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YSS->NSS).", "chr_id": "4", "chr_pos": "89927905", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y356", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q13201-1.344.344", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q13201-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q13201-1.366.366", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.366.366", "start_pos": 366, "end_pos": 366, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1178531970", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1178531970", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1178531970", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1178531970#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1178531970", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1178531970", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SLTVNDVRNTYSSLEGKVSE", "down_seq": "KSREFQSLLKGLKSKSINVL", "snv": [ { "evidence": [ { "id": "rs1178531970", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1178531970" }, { "id": "rs1178531970", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1178531970#frequency_tab" }, { "id": "rs1178531970", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1178531970" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DKS->NKS).", "chr_id": "4", "chr_pos": "89927935", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D366", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q13201-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q13201-1.356.356", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.421.421", "start_pos": 421, "end_pos": 421, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "DMQETVAQLFKTVSSLSEDL", "down_seq": "STRQIIQKVNESVVSIAAQQ", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "89934941", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E421", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q13201-1.417.417", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13201-1.422.422", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q13201-1.431.431", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q13201-1.433.433", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.433.433", "start_pos": 433, "end_pos": 433, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1722558454", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722558454", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1722558454", "url": "https://www.ensembl.org/id/rs1722558454", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VSSLSEDLESTRQIIQKVNE", "down_seq": "VVSIAAQQKFVLVQENRPTL", "snv": [ { "evidence": [ { "id": "rs1722558454", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722558454" }, { "id": "rs1722558454", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1722558454" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NES->NEP).", "chr_id": "4", "chr_pos": "89934977", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S433", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NES->NEY).", "chr_id": "4", "chr_pos": "89934978", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S433", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q13201-1.417.417", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q13201-1.421.421", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q13201-1.422.422", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13201-1.431.431", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.463.463", "start_pos": 463, "end_pos": 463, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1228178026", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1228178026", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1228178026", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1228178026", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "FVLVQENRPTLTDIVELRNH", "down_seq": "VNVRQEMTLTCEKPIKELEV", "snv": [ { "evidence": [ { "id": "rs1228178026", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1228178026" }, { "id": "rs1228178026", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1228178026" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NHI->NHT).", "chr_id": "4", "chr_pos": "89935068", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I463", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.49.49", "start_pos": 49, "end_pos": 49, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1431093054", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1431093054", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1431093054", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1431093054", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1431093054", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1431093054", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "IPEDGNSQKTMPSASVPPNK", "down_seq": "QSLQILPTTRVMSAEIATTP", "snv": [ { "evidence": [ { "id": "rs1431093054", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1431093054" }, { "id": "rs1431093054", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1431093054" }, { "id": "rs1431093054", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1431093054" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NKI->NKT).", "chr_id": "4", "chr_pos": "89895117", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I49", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q13201-1.63.63", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.533.533", "start_pos": 533, "end_pos": 533, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1177734121", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1177734121", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1177734121", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1177734121#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1177734121", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1177734121", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LKEVHEQLLSTEQVSDQKNA", "down_seq": "AAESVSNNVTEYMSTLHENI", "snv": [ { "evidence": [ { "id": "rs1177734121", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1177734121" }, { "id": "rs1177734121", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1177734121#frequency_tab" }, { "id": "rs1177734121", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1177734121" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NAP->NAS).", "chr_id": "4", "chr_pos": "89935277", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P533", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q13201-1.541.541", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.555.555", "start_pos": 555, "end_pos": 555, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "AESVSNNVTEYMSTLHENIK", "down_seq": "QSLMMLQMFEDLHIQESKIN", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KQS->NQS).", "chr_id": "4", "chr_pos": "89935345", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K555", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q13201-1.541.541", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q13201-1.573.573", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.579.579", "start_pos": 579, "end_pos": 579, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "MMLQMFEDLHIQESKINNLT", "down_seq": "SLEMEKESLRGECEDMLSKC", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "4", "chr_pos": "89935415", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V579", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q13201-1.573.573", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q13201-1.576.576", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.603.603", "start_pos": 603, "end_pos": 603, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1722588539", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722588539", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1722588539", "url": "https://www.ensembl.org/id/rs1722588539", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "MEKESLRGECEDMLSKCRND", "down_seq": "KFQLKDTEENLHVLNQTLAE", "snv": [ { "evidence": [ { "id": "rs1722588539", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722588539" }, { "id": "rs1722588539", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1722588539" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDF->NDS).", "chr_id": "4", "chr_pos": "89935488", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F603", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q13201-1.608.608", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q13201-1.618.618", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q13201-1.620.620", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.608.608", "start_pos": 608, "end_pos": 608, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1553924454", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1553924454", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1553924454", "url": "https://www.ensembl.org/id/rs1553924454", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1553924454", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1553924454", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LRGECEDMLSKCRNDFKFQL", "down_seq": "DTEENLHVLNQTLAEVLFPM", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" }, { "id": "rs1553924454", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1553924454" }, { "id": "rs1553924454", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1553924454" }, { "id": "rs1553924454", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1553924454" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KDT->NDT).", "chr_id": "4", "chr_pos": "89935504", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K608", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q13201-1.603.603", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q13201-1.618.618", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q13201-1.620.620", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.620.620", "start_pos": 620, "end_pos": 620, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1722591929", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722591929", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1722591929", "url": "https://www.ensembl.org/id/rs1722591929", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RNDFKFQLKDTEENLHVLNQ", "down_seq": "LAEVLFPMDNKMDKMSEQLN", "snv": [ { "evidence": [ { "id": "rs1722591929", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722591929" }, { "id": "rs1722591929", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1722591929" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NQT->NQI).", "chr_id": "4", "chr_pos": "89935539", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T620", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q13201-1.603.603", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q13201-1.608.608", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13201-1.618.618", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q13201-1.632.632", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.632.632", "start_pos": 632, "end_pos": 632, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1235958769", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1235958769", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1235958769", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1235958769#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1235958769", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1235958769", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "ENLHVLNQTLAEVLFPMDNK", "down_seq": "DKMSEQLNDLTYDMEILQPL", "snv": [ { "evidence": [ { "id": "rs1235958769", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1235958769" }, { "id": "rs1235958769", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1235958769#frequency_tab" }, { "id": "rs1235958769", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1235958769" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKM->NKT).", "chr_id": "4", "chr_pos": "89935575", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M632", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q13201-1.618.618", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q13201-1.620.620", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q13201-1.641.641", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q13201-1.642.642", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.63.63", "start_pos": 63, "end_pos": 63, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SVPPNKIQSLQILPTTRVMS", "down_seq": "EIATTPEARTSEDSLLKSTL", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "4", "chr_pos": "89895159", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A63", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q13201-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q13201-1.73.73", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q13201-1.80.80", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.641.641", "start_pos": 641, "end_pos": 641, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1177890844", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1177890844", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1177890844", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1177890844", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1177890844", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1177890844", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LAEVLFPMDNKMDKMSEQLN", "down_seq": "LTYDMEILQPLLEQGASLRQ", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" }, { "id": "rs1177890844", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1177890844" }, { "id": "rs1177890844", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1177890844" }, { "id": "rs1177890844", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1177890844" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DLT->NLT).", "chr_id": "4", "chr_pos": "89935601", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D641", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q13201-1.632.632", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13201-1.642.642", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.642.642", "start_pos": 642, "end_pos": 642, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1476029496", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1476029496", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1476029496", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1476029496#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1476029496", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1476029496", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "AEVLFPMDNKMDKMSEQLND", "down_seq": "TYDMEILQPLLEQGASLRQT", "snv": [ { "evidence": [ { "id": "rs1476029496", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1476029496" }, { "id": "rs1476029496", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1476029496#frequency_tab" }, { "id": "rs1476029496", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1476029496" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDL->NDS).", "chr_id": "4", "chr_pos": "89935605", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L642", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q13201-1.632.632", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13201-1.641.641", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.720.720", "start_pos": 720, "end_pos": 720, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1722610448", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722610448", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1722610448", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1722610448#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1722610448", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1722610448", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "NLLRNEVQGRDDALERRINE", "down_seq": "ALEMEDGLNKTMTIINNAID", "snv": [ { "evidence": [ { "id": "rs1722610448", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722610448" }, { "id": "rs1722610448", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1722610448#frequency_tab" }, { "id": "rs1722610448", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1722610448" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "Y", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEY->NES).", "chr_id": "4", "chr_pos": "89935839", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y720", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q13201-1.729.729", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q13201-1.731.731", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q13201-1.732.732", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q13201-1.738.738", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q13201-1.739.739", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.731.731", "start_pos": 731, "end_pos": 731, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs770136397", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770136397", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770136397", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770136397", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs770136397", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770136397#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs770136397", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770136397", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DALERRINEYALEMEDGLNK", "down_seq": "MTIINNAIDFIQDNYALKET", "snv": [ { "evidence": [ { "id": "rs770136397", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770136397" }, { "id": "rs770136397", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770136397" }, { "id": "rs770136397", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770136397#frequency_tab" }, { "id": "rs770136397", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770136397" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKT->NKA).", "chr_id": "4", "chr_pos": "89935871", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T731", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q13201-1.720.720", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13201-1.729.729", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13201-1.732.732", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q13201-1.738.738", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q13201-1.739.739", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q13201-1.747.747", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.732.732", "start_pos": 732, "end_pos": 732, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "ALERRINEYALEMEDGLNKT", "down_seq": "TIINNAIDFIQDNYALKETL", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "M", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "4", "chr_pos": "89935875", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "M732", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q13201-1.720.720", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q13201-1.729.729", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13201-1.731.731", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q13201-1.738.738", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q13201-1.739.739", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q13201-1.747.747", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.738.738", "start_pos": 738, "end_pos": 738, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1185016798", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1185016798", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1185016798", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1185016798#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1185016798", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1185016798", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1185016798", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1185016798", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "NEYALEMEDGLNKTMTIINN", "down_seq": "IDFIQDNYALKETLSTIKDN", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" }, { "id": "rs1185016798", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1185016798" }, { "id": "rs1185016798", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1185016798#frequency_tab" }, { "id": "rs1185016798", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1185016798" }, { "id": "rs1185016798", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1185016798" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NNA->NNS).", "chr_id": "4", "chr_pos": "89935892", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A738", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q13201-1.720.720", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q13201-1.729.729", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q13201-1.731.731", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q13201-1.732.732", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13201-1.739.739", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q13201-1.747.747", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q13201-1.757.757", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.739.739", "start_pos": 739, "end_pos": 739, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs761605234", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761605234", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs761605234", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761605234", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs761605234", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761605234", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "EYALEMEDGLNKTMTIINNA", "down_seq": "DFIQDNYALKETLSTIKDNS", "snv": [ { "evidence": [ { "id": "rs761605234", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761605234" }, { "id": "rs761605234", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761605234" }, { "id": "rs761605234", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761605234" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NAI->NAT).", "chr_id": "4", "chr_pos": "89935896", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I739", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q13201-1.720.720", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q13201-1.729.729", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q13201-1.731.731", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q13201-1.732.732", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13201-1.738.738", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q13201-1.747.747", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q13201-1.757.757", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.747.747", "start_pos": 747, "end_pos": 747, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1722614204", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722614204", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1722614204", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1722614204#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GLNKTMTIINNAIDFIQDNY", "down_seq": "LKETLSTIKDNSEIHHKCTS", "snv": [ { "evidence": [ { "id": "rs1722614204", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722614204" }, { "id": "rs1722614204", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1722614204#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NYA->NYS).", "chr_id": "4", "chr_pos": "89935919", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A747", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q13201-1.729.729", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q13201-1.731.731", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q13201-1.732.732", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q13201-1.738.738", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q13201-1.739.739", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q13201-1.757.757", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.757.757", "start_pos": 757, "end_pos": 757, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1264670018", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1264670018", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1264670018", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1264670018#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1264670018", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1264670018", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1264670018", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1264670018", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "NAIDFIQDNYALKETLSTIK", "down_seq": "NSEIHHKCTSDMETILTFIP", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" }, { "id": "rs1264670018", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1264670018" }, { "id": "rs1264670018", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1264670018#frequency_tab" }, { "id": "rs1264670018", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1264670018" }, { "id": "rs1264670018", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1264670018" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DNS->NNS).", "chr_id": "4", "chr_pos": "89935949", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D757", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q13201-1.738.738", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q13201-1.739.739", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q13201-1.747.747", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q13201-1.768.768", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.768.768", "start_pos": 768, "end_pos": 768, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LKETLSTIKDNSEIHHKCTS", "down_seq": "METILTFIPQFHRLNDSIQT", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "89935982", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D768", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q13201-1.757.757", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q13201-1.783.783", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q13201-1.785.785", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.785.785", "start_pos": 785, "end_pos": 785, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1722620684", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722620684", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1722620684", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1722620684#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CTSDMETILTFIPQFHRLND", "down_seq": "IQTLVNDNQRYNFVLQVAKT", "snv": [ { "evidence": [ { "id": "rs1722620684", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722620684" }, { "id": "rs1722620684", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1722620684#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NDS->NDP).", "chr_id": "4", "chr_pos": "89936033", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S785", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q13201-1.768.768", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13201-1.783.783", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q13201-1.793.793", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q13201-1.794.794", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q13201-1.795.795", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.793.793", "start_pos": 793, "end_pos": 793, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1451632351", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1451632351", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1451632351", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1451632351#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1451632351", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1451632351", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LTFIPQFHRLNDSIQTLVND", "down_seq": "QRYNFVLQVAKTLAGIPRDE", "snv": [ { "evidence": [ { "id": "rs1451632351", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1451632351" }, { "id": "rs1451632351", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1451632351#frequency_tab" }, { "id": "rs1451632351", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1451632351" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDN->NDS).", "chr_id": "4", "chr_pos": "89936058", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N793", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NDN->NDT).", "chr_id": "4", "chr_pos": "89936058", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N793", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q13201-1.783.783", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q13201-1.785.785", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13201-1.794.794", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q13201-1.795.795", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.794.794", "start_pos": 794, "end_pos": 794, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "TFIPQFHRLNDSIQTLVNDN", "down_seq": "RYNFVLQVAKTLAGIPRDEK", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "Q", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "4", "chr_pos": "89936062", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Q794", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q13201-1.783.783", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q13201-1.785.785", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13201-1.793.793", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13201-1.795.795", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.795.795", "start_pos": 795, "end_pos": 795, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FIPQFHRLNDSIQTLVNDNQ", "down_seq": "YNFVLQVAKTLAGIPRDEKL", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NQR->NQT).", "chr_id": "4", "chr_pos": "89936064", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "R795", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q13201-1.783.783", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q13201-1.785.785", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13201-1.793.793", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13201-1.794.794", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.80.80", "start_pos": 80, "end_pos": 80, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1457687214", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1457687214", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1457687214", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1457687214", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VMSAEIATTPEARTSEDSLL", "down_seq": "STLPPSETSAPAEGVRNQTL", "snv": [ { "evidence": [ { "id": "rs1457687214", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1457687214" }, { "id": "rs1457687214", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1457687214" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KST->NST).", "chr_id": "4", "chr_pos": "89895211", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K80", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q13201-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q13201-1.73.73", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q13201-1.97.111", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q13201-1.97.97", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.818.818", "start_pos": 818, "end_pos": 818, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201780689", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201780689", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201780689", "url": "https://www.ensembl.org/id/rs201780689", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FVLQVAKTLAGIPRDEKLNQ", "down_seq": "NFQKMYQMFNETTSQVRKYQ", "snv": [ { "evidence": [ { "id": "rs201780689", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201780689" }, { "id": "rs201780689", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs201780689" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NQS->NQY).", "chr_id": "4", "chr_pos": "89936133", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S818", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q13201-1.816.816", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q13201-1.828.828", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q13201-1.830.830", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.830.830", "start_pos": 830, "end_pos": 830, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs138633719", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138633719", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs138633719", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs138633719", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs138633719", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138633719", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs138633719", "url": "https://www.ncbi.nlm.nih.gov/snp/rs138633719#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs138633719", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138633719", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs138633719", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs138633719", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PRDEKLNQSNFQKMYQMFNE", "down_seq": "TSQVRKYQQNMSHLEEKLLL", "snv": [ { "evidence": [ { "id": "rs138633719", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138633719" }, { "id": "rs138633719", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs138633719" }, { "id": "rs138633719", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138633719" }, { "id": "rs138633719", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs138633719#frequency_tab" }, { "id": "rs138633719", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138633719" }, { "id": "rs138633719", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs138633719" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NET->NEI).", "chr_id": "4", "chr_pos": "89936169", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T830", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q13201-1.816.816", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q13201-1.818.818", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13201-1.828.828", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q13201-1.840.840", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q13201-1.842.842", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.842.842", "start_pos": 842, "end_pos": 842, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1483189147", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1483189147", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1483189147", "url": "https://www.ensembl.org/id/rs1483189147", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs548245722", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548245722", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs548245722", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs548245722", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs548245722", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548245722", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs548245722", "url": "https://www.ncbi.nlm.nih.gov/snp/rs548245722#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs548245722", "url": "http://gnomad.broadinstitute.org/awesome?query=rs548245722", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KMYQMFNETTSQVRKYQQNM", "down_seq": "HLEEKLLLTTKISKNFETRL", "snv": [ { "evidence": [ { "id": "rs1483189147", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1483189147" }, { "id": "rs1483189147", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1483189147" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NMS->NMN).", "chr_id": "4", "chr_pos": "89936205", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S842", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" }, { "id": "rs548245722", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548245722" }, { "id": "rs548245722", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs548245722" }, { "id": "rs548245722", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548245722" }, { "id": "rs548245722", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs548245722#frequency_tab" }, { "id": "rs548245722", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs548245722" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NMS->NMR).", "chr_id": "4", "chr_pos": "89936206", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S842", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q13201-1.828.828", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q13201-1.830.830", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13201-1.840.840", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.870.870", "start_pos": 870, "end_pos": 870, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs887723150", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs887723150", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs887723150", "url": "http://gnomad.broadinstitute.org/awesome?query=rs887723150", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LTTKISKNFETRLQDIESKV", "down_seq": "QTLIPYYISVKKGSVVTNER", "snv": [ { "evidence": [ { "id": "rs887723150", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs887723150" }, { "id": "rs887723150", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs887723150" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TQT->NQT).", "chr_id": "4", "chr_pos": "89936289", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T870", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q13201-1.872.872", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q13201-1.890.890", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.872.872", "start_pos": 872, "end_pos": 872, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TKISKNFETRLQDIESKVTQ", "down_seq": "LIPYYISVKKGSVVTNERDQ", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "4", "chr_pos": "89936295", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T872", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q13201-1.870.870", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q13201-1.890.890", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.890.890", "start_pos": 890, "end_pos": 890, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs778676840", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778676840", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778676840", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778676840", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778676840", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778676840#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs778676840", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778676840", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs768617103", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768617103", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768617103", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768617103", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs768617103", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768617103", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TQTLIPYYISVKKGSVVTNE", "down_seq": "DQALQLQVLNSRFKALEAKS", "snv": [ { "evidence": [ { "id": "rs778676840", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778676840" }, { "id": "rs778676840", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778676840" }, { "id": "rs778676840", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778676840#frequency_tab" }, { "id": "rs778676840", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778676840" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NER->NES).", "chr_id": "4", "chr_pos": "89936350", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R890", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs768617103", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768617103" }, { "id": "rs768617103", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768617103" }, { "id": "rs768617103", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768617103" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NER->NET).", "chr_id": "4", "chr_pos": "89936349", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R890", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q13201-1.870.870", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q13201-1.872.872", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.917.917", "start_pos": 917, "end_pos": 917, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "QVLNSRFKALEAKSIHLSIN", "down_seq": "FSLNKTLHEVLTMCHNASTS", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "4", "frequency": "0.2", "sequence_org": "F", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "89936431", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "F917", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q13201-1.921.921", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q13201-1.923.923", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q13201-1.926.926", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q13201-1.933.933", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q13201-1.934.934", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q13201-1.935.935", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.923.923", "start_pos": 923, "end_pos": 923, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs776154307", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776154307", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776154307", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776154307", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776154307", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776154307#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs776154307", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776154307", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "FKALEAKSIHLSINFFSLNK", "down_seq": "LHEVLTMCHNASTSVSELNA", "snv": [ { "evidence": [ { "id": "rs776154307", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776154307" }, { "id": "rs776154307", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776154307" }, { "id": "rs776154307", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776154307#frequency_tab" }, { "id": "rs776154307", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776154307" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKT->NKI).", "chr_id": "4", "chr_pos": "89936448", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T923", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q13201-1.917.917", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13201-1.921.921", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q13201-1.926.926", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q13201-1.933.933", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q13201-1.934.934", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q13201-1.935.935", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q13201-1.942.942", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.926.926", "start_pos": 926, "end_pos": 926, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "LEAKSIHLSINFFSLNKTLH", "down_seq": "VLTMCHNASTSVSELNATIP", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "4", "chr_pos": "89936456", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E926", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q13201-1.917.917", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q13201-1.921.921", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q13201-1.923.923", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q13201-1.933.933", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q13201-1.934.934", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q13201-1.935.935", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q13201-1.942.942", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.934.934", "start_pos": 934, "end_pos": 934, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs372641278", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372641278", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs372641278", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372641278", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs372641278", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372641278#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs372641278", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372641278", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SINFFSLNKTLHEVLTMCHN", "down_seq": "STSVSELNATIPKWIKHSLP", "snv": [ { "evidence": [ { "id": "rs372641278", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372641278" }, { "id": "rs372641278", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372641278" }, { "id": "rs372641278", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372641278#frequency_tab" }, { "id": "rs372641278", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372641278" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NAS->NPS).", "chr_id": "4", "chr_pos": "89936480", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A934", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q13201-1.917.917", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q13201-1.921.921", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q13201-1.923.923", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q13201-1.926.926", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13201-1.933.933", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13201-1.935.935", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q13201-1.942.942", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.935.935", "start_pos": 935, "end_pos": 935, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752526555", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752526555", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752526555", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752526555", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752526555", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752526555#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs752526555", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752526555", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1329212890", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1329212890", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1329212890", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1329212890", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "INFFSLNKTLHEVLTMCHNA", "down_seq": "TSVSELNATIPKWIKHSLPD", "snv": [ { "evidence": [ { "id": "rs752526555", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752526555" }, { "id": "rs752526555", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752526555" }, { "id": "rs752526555", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752526555#frequency_tab" }, { "id": "rs752526555", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752526555" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NAS->NAA).", "chr_id": "4", "chr_pos": "89936483", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S935", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1329212890", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1329212890" }, { "id": "rs1329212890", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1329212890" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NAS->NAF).", "chr_id": "4", "chr_pos": "89936484", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S935", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q13201-1.917.917", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q13201-1.921.921", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q13201-1.923.923", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q13201-1.926.926", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q13201-1.933.933", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13201-1.934.934", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q13201-1.942.942", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.983.983", "start_pos": 983, "end_pos": 983, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs771272615", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771272615", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771272615", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771272615", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771272615", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771272615#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771272615", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771272615", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LTEFVEPIIQIKTQAALSNL", "down_seq": "CCIDRSLPGSLANVVKSQKQ", "snv": [ { "evidence": [ { "id": "rs771272615", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771272615" }, { "id": "rs771272615", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771272615" }, { "id": "rs771272615", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771272615#frequency_tab" }, { "id": "rs771272615", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771272615" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->NLI).", "chr_id": "4", "chr_pos": "89936628", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T983", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q13201-1.981.981", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q13201-1.987.987", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.987.987", "start_pos": 987, "end_pos": 987, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13201", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1722652473", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722652473", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1722652473", "url": "https://www.ensembl.org/id/rs1722652473", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1722652473", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1722652473", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VEPIIQIKTQAALSNLTCCI", "down_seq": "RSLPGSLANVVKSQKQVKSL", "snv": [ { "evidence": [ { "id": "Q13201", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13201" }, { "id": "rs1722652473", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1722652473" }, { "id": "rs1722652473", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1722652473" }, { "id": "rs1722652473", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1722652473" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DRS->NRS).", "chr_id": "4", "chr_pos": "89936639", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D987", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q13201-1.981.981", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q13201-1.983.983", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q13201-1.417.417", "start_pos": 417, "end_pos": 417, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Motif-specific sampling of phosphoproteomes.", "journal": "Journal of proteome research", "date": "2008", "authors": "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "evidence": [ { "database": "iPTMnet", "id": "Q13201-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13201-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "Q13201", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13201", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IFQNDMQETVAQLFKTVSSL", "down_seq": "EDLESTRQIIQKVNESVVSI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q13201", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13201" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser417" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q13201-1.421.421", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q13201-1.422.422", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q13201-1.431.431", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q13201-1.433.433", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13201-1.422.422", "start_pos": 422, "end_pos": 422, "uniprot_canonical_ac": "Q13201-1", "length": 1228, "uniprot_id": "MMRN1_HUMAN", "protein_name": "Multimerin-1", "refseq_ac": "NP_031377", "refseq_name": "multimerin-1 isoform 1 precursor", "gene_name": "MMRN1", "gene_names_uniprotkb": "MMRN1; ECM; EMILIN4; GPIA*; MMRN", "gene_names_refseq": "ECM; EMILIN4; GPIa*; MMRN1; MMRN", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13201", "url": "https://www.uniprot.org/uniprotkb/Q13201" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Motif-specific sampling of phosphoproteomes.", "journal": "Journal of proteome research", "date": "2008", "authors": "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "evidence": [ { "database": "iPTMnet", "id": "Q13201-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13201-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "Q13201", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13201", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MQETVAQLFKTVSSLSEDLE", "down_seq": "TRQIIQKVNESVVSIAAQQK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q13201", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13201" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Ser422" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "816", "end_pos": "816" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "111" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "981", "end_pos": "981" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "216", "end_pos": "216" }, { "start_pos": "265", "end_pos": "265" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1015", "end_pos": "1015" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1022", "end_pos": "1022" }, { "start_pos": "1037", "end_pos": "1037" }, { "start_pos": "1049", "end_pos": "1049" }, { "start_pos": "1055", "end_pos": "1055" }, { "start_pos": "1058", "end_pos": "1058" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1075", "end_pos": "1075" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1122", "end_pos": "1122" }, { "start_pos": "1148", "end_pos": "1148" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "1151", "end_pos": "1151" }, { "start_pos": "1152", "end_pos": "1152" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "1177", "end_pos": "1177" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "296", "end_pos": "296" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "541", "end_pos": "541" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "618", "end_pos": "618" }, { "start_pos": "620", "end_pos": "620" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "680", "end_pos": "680" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "729", "end_pos": "729" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "738", "end_pos": "738" }, { "start_pos": "739", "end_pos": "739" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "747", "end_pos": "747" }, { "start_pos": "757", "end_pos": "757" }, { "start_pos": "768", "end_pos": "768" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "785", "end_pos": "785" }, { "start_pos": "793", "end_pos": "793" }, { "start_pos": "794", "end_pos": "794" }, { "start_pos": "795", "end_pos": "795" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "828", "end_pos": "828" }, { "start_pos": "830", "end_pos": "830" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "842", "end_pos": "842" }, { "start_pos": "870", "end_pos": "870" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "890", "end_pos": "890" }, { "start_pos": "917", "end_pos": "917" }, { "start_pos": "921", "end_pos": "921" }, { "start_pos": "923", "end_pos": "923" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "933", "end_pos": "933" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "942", "end_pos": "942" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "983", "end_pos": "983" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "417", "end_pos": "417" }, { "start_pos": "422", "end_pos": "422" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q13201-1.417.417", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13201-1.421.421", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q13201-1.431.431", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q13201-1.433.433", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14934-1.124.124", "start_pos": 124, "end_pos": 124, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1399617431", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1399617431", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1399617431", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1399617431", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q14934", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14934", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1399617431", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1399617431", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GAGGGRVLECPSIRITSISP", "down_seq": "PEPPAALEDNPDAWGDGSPR", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr124", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1399617431", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1399617431" }, { "id": "rs1399617431", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1399617431" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->K).", "chr_id": "14", "chr_pos": "24369769", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T124", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q14934", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14934" }, { "id": "rs1399617431", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1399617431" }, { "id": "rs1399617431", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1399617431" }, { "id": "rs1399617431", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1399617431" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->M).", "chr_id": "14", "chr_pos": "24369769", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T124", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14934-1.256.256", "start_pos": 256, "end_pos": 256, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs972744763", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs972744763", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs972744763", "url": "https://www.ensembl.org/id/rs972744763", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PSPGGRGPEDSWLLLSAPGP", "down_seq": "PASPRPASPCGKRRYSSSGT", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr256", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs972744763", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs972744763" }, { "id": "rs972744763", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs972744763" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->P).", "chr_id": "14", "chr_pos": "24370164", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T256", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q14934-1.259.259", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14934-1.276.276", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14934-1.276.276", "start_pos": 276, "end_pos": 276, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1421490567", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1421490567", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1421490567", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1421490567", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1594704442", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1594704442", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1594704442", "url": "https://www.ensembl.org/id/rs1594704442", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TPASPRPASPCGKRRYSSSG", "down_seq": "PSSASPALSRRGSLGEEGSE", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr276", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1421490567", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1421490567" }, { "id": "rs1421490567", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1421490567" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->N).", "chr_id": "14", "chr_pos": "24370225", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T276", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1594704442", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1594704442" }, { "id": "rs1594704442", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1594704442" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->P).", "chr_id": "14", "chr_pos": "24370224", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T276", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14934-1.256.256", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q14934-1.259.259", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14934-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q14934-1.289.289", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14934-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q14934", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14934" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14934", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14934", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "Q14934", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14934" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14934-1.168.168", "start_pos": 168, "end_pos": 168, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of NFATc4 by p38 mitogen-activated protein kinases.", "journal": "Molecular and cellular biology", "date": "2002", "authors": "Yang TT, Xiong Q, Enslen H, Davis RJ, Chow CW", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "iPTMnet", "id": "Q14934-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934-1" } ], "reference": [ { "type": "PubMed", "id": "11997522", "url": "https://glygen.org/publication/PubMed/11997522" } ] }, { "title": "Integration of protein kinases mTOR and extracellular signal-regulated kinase 5 in regulating nucleocytoplasmic localization of NFATc4.", "journal": "Molecular and cellular biology", "date": "2008", "authors": "Yang TT, Yu RY, Agadir A, Gao GJ, Campos-Gonzalez R, Tournier C, Chow CW", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" } ], "reference": [ { "type": "PubMed", "id": "18347059", "url": "https://glygen.org/publication/PubMed/18347059" } ] }, { "title": "Tissue type-specific modulation of ER transcriptional activity by NFAT3.", "journal": "Biochemical and biophysical research communications", "date": "2007", "authors": "Zhang H, Wang X, Li J, Zhu J, Xie X, Yuan B, Yang Z, Zeng M, Jiang Z, Li J, Huang C, Ye Q", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" } ], "reference": [ { "type": "PubMed", "id": "17194453", "url": "https://glygen.org/publication/PubMed/17194453" } ] }, { "title": "Neuritin Up-regulates Kv4.2 alpha-Subunit of Potassium Channel Expression and Affects Neuronal Excitability by Regulating the Calcium-Calcineurin-NFATc4 Signaling Pathway.", "journal": "The Journal of biological chemistry", "date": "2016", "authors": "Yao JJ, Zhao QR, Liu DD, Chow CW, Mei YA", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" } ], "reference": [ { "type": "PubMed", "id": "27307045", "url": "https://glygen.org/publication/PubMed/27307045" } ] } ], "crossref": [ { "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11997522", "url": "https://glygen.org/publication/PubMed/11997522", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18347059", "url": "https://glygen.org/publication/PubMed/18347059", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17194453", "url": "https://glygen.org/publication/PubMed/17194453", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27307045", "url": "https://glygen.org/publication/PubMed/27307045", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PPEGFGGYREAGGQGGGAFF", "down_seq": "PSPGSSSLSSWSFFSDASDE", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Promotes nuclear localization and increases transcriptional activity; when associated with A-170.", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "PubMed", "id": "11997522", "url": "https://glygen.org/publication/PubMed/11997522" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "O15264-1", "kinase_gene_name": "MAPK13", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "11997522", "url": "https://glygen.org/publication/PubMed/11997522" } ], "site_lbl": "Ser168" }, { "kinase_uniprot_canonical_ac": "P53778-1", "kinase_gene_name": "MAPK12", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "11997522", "url": "https://glygen.org/publication/PubMed/11997522" } ], "site_lbl": "Ser168" }, { "kinase_uniprot_canonical_ac": "Q13164-1", "kinase_gene_name": "MAPK7", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "18347059", "url": "https://glygen.org/publication/PubMed/18347059" } ], "site_lbl": "Ser168" }, { "kinase_uniprot_canonical_ac": "Q15759-1", "kinase_gene_name": "MAPK11", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "11997522", "url": "https://glygen.org/publication/PubMed/11997522" } ], "site_lbl": "Ser168" }, { "kinase_uniprot_canonical_ac": "Q16539-1", "kinase_gene_name": "MAPK14", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "11997522", "url": "https://glygen.org/publication/PubMed/11997522" } ], "site_lbl": "Ser168" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by MAPK7 and MAPK14", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "18347059", "url": "https://glygen.org/publication/PubMed/18347059" }, { "database": "PubMed", "id": "17194453", "url": "https://glygen.org/publication/PubMed/17194453" }, { "database": "PubMed", "id": "27307045", "url": "https://glygen.org/publication/PubMed/27307045" }, { "database": "PubMed", "id": "11997522", "url": "https://glygen.org/publication/PubMed/11997522" } ], "site_lbl": "Ser168" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q14934-1.170.170", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q14934-1.184.184", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14934-1.170.170", "start_pos": 170, "end_pos": 170, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of NFATc4 by p38 mitogen-activated protein kinases.", "journal": "Molecular and cellular biology", "date": "2002", "authors": "Yang TT, Xiong Q, Enslen H, Davis RJ, Chow CW", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "iPTMnet", "id": "Q14934-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934-1" } ], "reference": [ { "type": "PubMed", "id": "11997522", "url": "https://glygen.org/publication/PubMed/11997522" } ] }, { "title": "Integration of protein kinases mTOR and extracellular signal-regulated kinase 5 in regulating nucleocytoplasmic localization of NFATc4.", "journal": "Molecular and cellular biology", "date": "2008", "authors": "Yang TT, Yu RY, Agadir A, Gao GJ, Campos-Gonzalez R, Tournier C, Chow CW", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" } ], "reference": [ { "type": "PubMed", "id": "18347059", "url": "https://glygen.org/publication/PubMed/18347059" } ] }, { "title": "Tissue type-specific modulation of ER transcriptional activity by NFAT3.", "journal": "Biochemical and biophysical research communications", "date": "2007", "authors": "Zhang H, Wang X, Li J, Zhu J, Xie X, Yuan B, Yang Z, Zeng M, Jiang Z, Li J, Huang C, Ye Q", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" } ], "reference": [ { "type": "PubMed", "id": "17194453", "url": "https://glygen.org/publication/PubMed/17194453" } ] }, { "title": "Neuritin Up-regulates Kv4.2 alpha-Subunit of Potassium Channel Expression and Affects Neuronal Excitability by Regulating the Calcium-Calcineurin-NFATc4 Signaling Pathway.", "journal": "The Journal of biological chemistry", "date": "2016", "authors": "Yao JJ, Zhao QR, Liu DD, Chow CW, Mei YA", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" } ], "reference": [ { "type": "PubMed", "id": "27307045", "url": "https://glygen.org/publication/PubMed/27307045" } ] } ], "crossref": [ { "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11997522", "url": "https://glygen.org/publication/PubMed/11997522", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18347059", "url": "https://glygen.org/publication/PubMed/18347059", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17194453", "url": "https://glygen.org/publication/PubMed/17194453", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27307045", "url": "https://glygen.org/publication/PubMed/27307045", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EGFGGYREAGGQGGGAFFSP", "down_seq": "PGSSSLSSWSFFSDASDEAA", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Promotes nuclear localization and increases transcriptional activity; when associated with A-168.", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "PubMed", "id": "11997522", "url": "https://glygen.org/publication/PubMed/11997522" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "O15264-1", "kinase_gene_name": "MAPK13", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "11997522", "url": "https://glygen.org/publication/PubMed/11997522" } ], "site_lbl": "Ser170" }, { "kinase_uniprot_canonical_ac": "P53778-1", "kinase_gene_name": "MAPK12", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "11997522", "url": "https://glygen.org/publication/PubMed/11997522" } ], "site_lbl": "Ser170" }, { "kinase_uniprot_canonical_ac": "Q13164-1", "kinase_gene_name": "MAPK7", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "18347059", "url": "https://glygen.org/publication/PubMed/18347059" } ], "site_lbl": "Ser170" }, { "kinase_uniprot_canonical_ac": "Q15759-1", "kinase_gene_name": "MAPK11", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "11997522", "url": "https://glygen.org/publication/PubMed/11997522" } ], "site_lbl": "Ser170" }, { "kinase_uniprot_canonical_ac": "Q16539-1", "kinase_gene_name": "MAPK14", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "11997522", "url": "https://glygen.org/publication/PubMed/11997522" } ], "site_lbl": "Ser170" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by MAPK7 and MAPK14", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "18347059", "url": "https://glygen.org/publication/PubMed/18347059" }, { "database": "PubMed", "id": "17194453", "url": "https://glygen.org/publication/PubMed/17194453" }, { "database": "PubMed", "id": "27307045", "url": "https://glygen.org/publication/PubMed/27307045" }, { "database": "PubMed", "id": "11997522", "url": "https://glygen.org/publication/PubMed/11997522" } ], "site_lbl": "Ser170" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q14934-1.168.168", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14934-1.184.184", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14934-1.213.213", "start_pos": 213, "end_pos": 213, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Nuclear factor of activated T3 is a negative regulator of Ras-JNK1/2-AP-1 induced cell transformation.", "journal": "Cancer research", "date": "2007", "authors": "Yao K, Cho YY, Bergen HR 3rd, Madden BJ, Choi BY, Ma WY, Bode AM, Dong Z", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" } ], "reference": [ { "type": "PubMed", "id": "17875713", "url": "https://glygen.org/publication/PubMed/17875713" } ] }, { "title": "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Pan C, Olsen JV, Daub H, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q14934-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17875713", "url": "https://glygen.org/publication/PubMed/17875713", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AACDEVESELNEAASRFGLG", "down_seq": "PLPSPRASPRPWTPEDPWSL", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Marked decrease in phosphorylation by MAPK8 or MAPK9. Complete loss of phosphorylation by MAPK8 or MAPK9, but no effect on MAPK8/9-binding; when associated with A-217. Decreased transcriptional activity; when associated with A-217.", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "PubMed", "id": "17875713", "url": "https://glygen.org/publication/PubMed/17875713" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P45983-1", "kinase_gene_name": "MAPK8", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "17875713", "url": "https://glygen.org/publication/PubMed/17875713" } ], "site_lbl": "Ser213" }, { "kinase_uniprot_canonical_ac": "P45984-1", "kinase_gene_name": "MAPK9", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "17875713", "url": "https://glygen.org/publication/PubMed/17875713" } ], "site_lbl": "Ser213" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by MAPK8 and MAPK9", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "17875713", "url": "https://glygen.org/publication/PubMed/17875713" } ], "site_lbl": "Ser213" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q14934-1.217.217", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14934-1.221.221", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14934-1.217.217", "start_pos": 217, "end_pos": 217, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Nuclear factor of activated T3 is a negative regulator of Ras-JNK1/2-AP-1 induced cell transformation.", "journal": "Cancer research", "date": "2007", "authors": "Yao K, Cho YY, Bergen HR 3rd, Madden BJ, Choi BY, Ma WY, Bode AM, Dong Z", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" } ], "reference": [ { "type": "PubMed", "id": "17875713", "url": "https://glygen.org/publication/PubMed/17875713" } ] }, { "title": "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Pan C, Olsen JV, Daub H, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q14934-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17875713", "url": "https://glygen.org/publication/PubMed/17875713", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EVESELNEAASRFGLGSPLP", "down_seq": "PRASPRPWTPEDPWSLYGPS", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Marked decrease in phosphorylation by MAPK8 or MAPK9. Complete loss of phosphorylation by MAPK8 or MAPK9, but no effect on MAPK8/9-binding; when associated with A-213. Decreased transcriptional activity; when associated with A-213.", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "PubMed", "id": "17875713", "url": "https://glygen.org/publication/PubMed/17875713" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P45983-1", "kinase_gene_name": "MAPK8", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "17875713", "url": "https://glygen.org/publication/PubMed/17875713" } ], "site_lbl": "Ser217" }, { "kinase_uniprot_canonical_ac": "P45984-1", "kinase_gene_name": "MAPK9", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "17875713", "url": "https://glygen.org/publication/PubMed/17875713" } ], "site_lbl": "Ser217" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by MAPK8 and MAPK9", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "17875713", "url": "https://glygen.org/publication/PubMed/17875713" } ], "site_lbl": "Ser217" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q14934-1.213.213", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14934-1.221.221", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14934-1.234.234", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14934-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14934", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14934", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GAFFSPSPGSSSLSSWSFFS", "down_seq": "ASDEAALYAACDEVESELNE", "snv": [ { "evidence": [ { "id": "Q14934", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14934" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DAS->NAS).", "chr_id": "14", "chr_pos": "24369948", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D184", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q14934-1.168.168", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q14934-1.170.170", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14934-1.286.286", "start_pos": 286, "end_pos": 286, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14934", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14934", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "CGKRRYSSSGTPSSASPALS", "down_seq": "RGSLGEEGSEPPPPPPLPLA", "snv": [ { "evidence": [ { "id": "Q14934", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14934" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "14", "chr_pos": "24370255", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R286", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q14934-1.276.276", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q14934-1.289.289", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14934-1.517.517", "start_pos": 517, "end_pos": 517, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs780733914", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780733914", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780733914", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780733914", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780733914", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780733914", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "YEAVVSGTKVLEMTLLPENN", "down_seq": "AANIDCAGILKLRNSDIELR", "snv": [ { "evidence": [ { "id": "rs780733914", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780733914" }, { "id": "rs780733914", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780733914" }, { "id": "rs780733914", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780733914" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNM->NNT).", "chr_id": "14", "chr_pos": "24373361", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M517", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q14934-1.518.518", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14934-1.518.518", "start_pos": 518, "end_pos": 518, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14934", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14934", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2139297754", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139297754", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2139297754", "url": "https://www.ensembl.org/id/rs2139297754", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "EAVVSGTKVLEMTLLPENNM", "down_seq": "ANIDCAGILKLRNSDIELRK", "snv": [ { "evidence": [ { "id": "Q14934", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14934" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NMA->NMS).", "chr_id": "14", "chr_pos": "24373363", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A518", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs2139297754", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139297754" }, { "id": "rs2139297754", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2139297754" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NMA->NMT).", "chr_id": "14", "chr_pos": "24373363", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A518", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q14934-1.517.517", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14934-1.549.549", "start_pos": 549, "end_pos": 549, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1451677725", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1451677725", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1451677725", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1451677725#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1451677725", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1451677725", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LRNSDIELRKGETDIGRKNT", "down_seq": "VRLVFRVHVPQGGGKVVSVQ", "snv": [ { "evidence": [ { "id": "rs1451677725", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1451677725" }, { "id": "rs1451677725", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1451677725#frequency_tab" }, { "id": "rs1451677725", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1451677725" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTR->NTC).", "chr_id": "14", "chr_pos": "24373780", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R549", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1451677725", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1451677725" }, { "id": "rs1451677725", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1451677725#frequency_tab" }, { "id": "rs1451677725", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1451677725" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTR->NTS).", "chr_id": "14", "chr_pos": "24373780", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R549", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14934-1.657.657", "start_pos": 657, "end_pos": 657, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs868502619", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs868502619", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs868502619", "url": "http://gnomad.broadinstitute.org/awesome?query=rs868502619", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "NRLQSNEVTLTLTVPEYSNK", "down_seq": "VSRPVQVYFYVSNGRRKRSP", "snv": [ { "evidence": [ { "id": "rs868502619", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs868502619" }, { "id": "rs868502619", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs868502619" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKR->NKS).", "chr_id": "14", "chr_pos": "24376016", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R657", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q14934-1.674.674", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q14934-1.676.676", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14934-1.674.674", "start_pos": 674, "end_pos": 674, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs773487308", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773487308", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773487308", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773487308", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773487308", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773487308#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs773487308", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773487308", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SNKRVSRPVQVYFYVSNGRR", "down_seq": "RSPTQSFRFLPVICKEEPLP", "snv": [ { "evidence": [ { "id": "rs773487308", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773487308" }, { "id": "rs773487308", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773487308" }, { "id": "rs773487308", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773487308#frequency_tab" }, { "id": "rs773487308", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773487308" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KRS->NRS).", "chr_id": "14", "chr_pos": "24376067", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K674", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q14934-1.657.657", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14934-1.676.676", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14934-1.863.863", "start_pos": 863, "end_pos": 863, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1385775956", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1385775956", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1385775956", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1385775956#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1385775956", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1385775956", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VGPGYGPGEGAPEQEKSRGG", "down_seq": "SSGFRDSVPIQGITLEEVSE", "snv": [ { "evidence": [ { "id": "rs1385775956", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1385775956" }, { "id": "rs1385775956", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1385775956#frequency_tab" }, { "id": "rs1385775956", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1385775956" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YSS->NSS).", "chr_id": "14", "chr_pos": "24376824", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y863", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14934-1.221.221", "start_pos": 221, "end_pos": 221, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Pan C, Olsen JV, Daub H, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q14934-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ELNEAASRFGLGSPLPSPRA", "down_seq": "PRPWTPEDPWSLYGPSPGGR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser221" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q14934-1.213.213", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14934-1.217.217", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q14934-1.234.234", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14934-1.234.234", "start_pos": 234, "end_pos": 234, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Pan C, Olsen JV, Daub H, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q14934-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "PLPSPRASPRPWTPEDPWSL", "down_seq": "GPSPGGRGPEDSWLLLSAPG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Tyr234" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q14934-1.217.217", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q14934-1.221.221", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14934-1.259.259", "start_pos": 259, "end_pos": 259, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of NFAT3 by CDK3 induces cell transformation and promotes tumor growth in skin cancer.", "journal": "Oncogene", "date": "2017", "authors": "Xiao T, Zhu JJ, Huang S, Peng C, He S, Du J, Hong R, Chen X, Bode AM, Jiang W, Dong Z, Zheng D", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" } ], "reference": [ { "type": "PubMed", "id": "27893713", "url": "https://glygen.org/publication/PubMed/27893713" } ] } ], "crossref": [ { "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "27893713", "url": "https://glygen.org/publication/PubMed/27893713", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GGRGPEDSWLLLSAPGPTPA", "down_seq": "PRPASPCGKRRYSSSGTPSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "27893713", "url": "https://glygen.org/publication/PubMed/27893713" } ], "site_lbl": "Ser259" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q14934-1.256.256", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14934-1.276.276", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14934-1.289.289", "start_pos": 289, "end_pos": 289, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.", "journal": "Cell", "date": "2006", "authors": "Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q14934-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] }, { "title": "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Pan C, Olsen JV, Daub H, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q14934-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "RSK2 mediates muscle cell differentiation through regulation of NFAT3.", "journal": "The Journal of biological chemistry", "date": "2007", "authors": "Cho YY, Yao K, Bode AM, Bergen HR 3rd, Madden BJ, Oh SM, Ermakova S, Kang BS, Choi HS, Shim JH, Dong Z", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" } ], "reference": [ { "type": "PubMed", "id": "17213202", "url": "https://glygen.org/publication/PubMed/17213202" } ] } ], "crossref": [ { "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17213202", "url": "https://glygen.org/publication/PubMed/17213202", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RRYSSSGTPSSASPALSRRG", "down_seq": "LGEEGSEPPPPPPLPLARDP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by RPS6KA3", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "17213202", "url": "https://glygen.org/publication/PubMed/17213202" } ], "site_lbl": "Ser289" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q14934-1.276.276", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q14934-1.286.286", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14934-1.344.344", "start_pos": 344, "end_pos": 344, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "RSK2 mediates muscle cell differentiation through regulation of NFAT3.", "journal": "The Journal of biological chemistry", "date": "2007", "authors": "Cho YY, Yao K, Bode AM, Bergen HR 3rd, Madden BJ, Oh SM, Ermakova S, Kang BS, Choi HS, Shim JH, Dong Z", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" } ], "reference": [ { "type": "PubMed", "id": "17213202", "url": "https://glygen.org/publication/PubMed/17213202" } ] } ], "crossref": [ { "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17213202", "url": "https://glygen.org/publication/PubMed/17213202", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ESIPQKTRRTSSEQAVALPR", "down_seq": "EEPASCNGKLPLGAEESVAP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by RPS6KA3", "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" }, { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "17213202", "url": "https://glygen.org/publication/PubMed/17213202" } ], "site_lbl": "Ser344" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14934-1.676.676", "start_pos": 676, "end_pos": 676, "uniprot_canonical_ac": "Q14934-1", "length": 902, "uniprot_id": "NFAC4_HUMAN", "protein_name": "Nuclear factor of activated T-cells, cytoplasmic 4", "refseq_ac": "NP_001129494", "refseq_name": "nuclear factor of activated T-cells, cytoplasmic 4 isoform 1", "gene_name": "NFATC4", "gene_names_uniprotkb": "NFATC4; NFAT3", "gene_names_refseq": "NF-AT3; NF-ATC4; NFAT3; NFATC4", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14934", "url": "https://www.uniprot.org/uniprotkb/Q14934" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Recruitment of the extracellular signal-regulated kinase/ribosomal S6 kinase signaling pathway to the NFATc4 transcription activation complex.", "journal": "Molecular and cellular biology", "date": "2005", "authors": "Yang TT, Xiong Q, Graef IA, Crabtree GR, Chow CW", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" } ], "reference": [ { "type": "PubMed", "id": "15657420", "url": "https://glygen.org/publication/PubMed/15657420" } ] }, { "title": "Interleukin-18 suppresses adiponectin expression in 3T3-L1 adipocytes via a novel signal transduction pathway involving ERK1/2-dependent NFATc4 phosphorylation.", "journal": "The Journal of biological chemistry", "date": "2008", "authors": "Chandrasekar B, Patel DN, Mummidi S, Kim JW, Clark RA, Valente AJ", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" } ], "reference": [ { "type": "PubMed", "id": "18086672", "url": "https://glygen.org/publication/PubMed/18086672" } ] } ], "crossref": [ { "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15657420", "url": "https://glygen.org/publication/PubMed/15657420", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18086672", "url": "https://glygen.org/publication/PubMed/18086672", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KRVSRPVQVYFYVSNGRRKR", "down_seq": "PTQSFRFLPVICKEEPLPDS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P27361-1", "kinase_gene_name": "MAPK3", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "15657420", "url": "https://glygen.org/publication/PubMed/15657420" } ], "site_lbl": "Ser676" }, { "kinase_uniprot_canonical_ac": "P28482-1", "kinase_gene_name": "MAPK1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "15657420", "url": "https://glygen.org/publication/PubMed/15657420" } ], "site_lbl": "Ser676" }, { "kinase_uniprot_canonical_ac": "P51812-1", "kinase_gene_name": "RPS6KA3", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "15657420", "url": "https://glygen.org/publication/PubMed/15657420" } ], "site_lbl": "Ser676" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14934", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14934" }, { "database": "PubMed", "id": "18086672", "url": "https://glygen.org/publication/PubMed/18086672" } ], "site_lbl": "Ser676" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "276", "end_pos": "276" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "517", "end_pos": "517" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "674", "end_pos": "674" }, { "start_pos": "863", "end_pos": "863" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "168", "end_pos": "168" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "676", "end_pos": "676" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q14934-1.657.657", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14934-1.674.674", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q86T75-1.264.264", "start_pos": 264, "end_pos": 264, "uniprot_canonical_ac": "Q86T75-1", "length": 865, "uniprot_id": "NBPFB_HUMAN", "protein_name": "NBPF family member NBPF11", "refseq_ac": "NP_001095133", "refseq_name": "NBPF family member NBPF11 isoform b", "gene_name": "NBPF11", "gene_names_uniprotkb": "NBPF11; NBPF24", "gene_names_refseq": "NBPF11; NBPF24", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T75", "url": "https://www.uniprot.org/uniprotkb/Q86T75" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1667620314", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1667620314", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1667620314", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1667620314#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1667620314", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1667620314", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1571442825", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571442825", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1571442825", "url": "https://www.ensembl.org/id/rs1571442825", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RESSHDGCQDALNILPVPGP", "down_seq": "SSATNVSMVVSAGPLSSEKA", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr264", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1667620314", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1667620314" }, { "id": "rs1667620314", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1667620314#frequency_tab" }, { "id": "rs1667620314", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1667620314" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-gain (TSS->NSS); o-glyco-site-loss (T->N).", "chr_id": "1", "chr_pos": "148120698", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T264", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1667620314", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1667620314" }, { "id": "rs1667620314", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1667620314#frequency_tab" }, { "id": "rs1667620314", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1667620314" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "1", "chr_pos": "148120698", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T264", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1571442825", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1571442825" }, { "id": "rs1571442825", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1571442825" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->P).", "chr_id": "1", "chr_pos": "148120699", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T264", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "264", "end_pos": "264" } ] }, { "type": "snv", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "854", "end_pos": "854" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "220", "end_pos": "220" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T75-1.161.161", "start_pos": 161, "end_pos": 161, "uniprot_canonical_ac": "Q86T75-1", "length": 865, "uniprot_id": "NBPFB_HUMAN", "protein_name": "NBPF family member NBPF11", "refseq_ac": "NP_001095133", "refseq_name": "NBPF family member NBPF11 isoform b", "gene_name": "NBPF11", "gene_names_uniprotkb": "NBPF11; NBPF24", "gene_names_refseq": "NBPF11; NBPF24", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T75", "url": "https://www.uniprot.org/uniprotkb/Q86T75" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1190083834", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1190083834", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1190083834", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1190083834#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1190083834", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1190083834", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "GQDLQEQLAEGCRLAQHLVQ", "down_seq": "LSPENDEDEDEDVQVEEDEK", "snv": [ { "evidence": [ { "id": "rs1190083834", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1190083834" }, { "id": "rs1190083834", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1190083834#frequency_tab" }, { "id": "rs1190083834", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1190083834" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KLS->NLS).", "chr_id": "1", "chr_pos": "148123863", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K161", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "264", "end_pos": "264" } ] }, { "type": "snv", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "854", "end_pos": "854" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "220", "end_pos": "220" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T75-1.23.23", "start_pos": 23, "end_pos": 23, "uniprot_canonical_ac": "Q86T75-1", "length": 865, "uniprot_id": "NBPFB_HUMAN", "protein_name": "NBPF family member NBPF11", "refseq_ac": "NP_001095133", "refseq_name": "NBPF family member NBPF11 isoform b", "gene_name": "NBPF11", "gene_names_uniprotkb": "NBPF11; NBPF24", "gene_names_refseq": "NBPF11; NBPF24", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T75", "url": "https://www.uniprot.org/uniprotkb/Q86T75" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1235483684", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1235483684", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1235483684", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1235483684", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VSAGPWSSEKAEMNILEINE", "down_seq": "LRPQLAENKQQFRNLKERCF", "snv": [ { "evidence": [ { "id": "rs1235483684", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1235483684" }, { "id": "rs1235483684", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1235483684" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEK->NET).", "chr_id": "1", "chr_pos": "148126936", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K23", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "264", "end_pos": "264" } ] }, { "type": "snv", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "854", "end_pos": "854" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "220", "end_pos": "220" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T75-1.294.294", "start_pos": 294, "end_pos": 294, "uniprot_canonical_ac": "Q86T75-1", "length": 865, "uniprot_id": "NBPFB_HUMAN", "protein_name": "NBPF family member NBPF11", "refseq_ac": "NP_001095133", "refseq_name": "NBPF family member NBPF11 isoform b", "gene_name": "NBPF11", "gene_names_uniprotkb": "NBPF11; NBPF24", "gene_names_refseq": "NBPF11; NBPF24", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T75", "url": "https://www.uniprot.org/uniprotkb/Q86T75" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs75979253", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs75979253", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs75979253", "url": "https://www.ensembl.org/id/rs75979253", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VSAGPLSSEKAEMNILEINE", "down_seq": "LCPQLAEKKQQFRSLKEKCF", "snv": [ { "evidence": [ { "id": "rs75979253", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs75979253" }, { "id": "rs75979253", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs75979253" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KLC->NLC).", "chr_id": "1", "chr_pos": "148120607", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K294", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "264", "end_pos": "264" } ] }, { "type": "snv", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "854", "end_pos": "854" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "220", "end_pos": "220" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T75-1.432.432", "start_pos": 432, "end_pos": 432, "uniprot_canonical_ac": "Q86T75-1", "length": 865, "uniprot_id": "NBPFB_HUMAN", "protein_name": "NBPF family member NBPF11", "refseq_ac": "NP_001095133", "refseq_name": "NBPF family member NBPF11 isoform b", "gene_name": "NBPF11", "gene_names_uniprotkb": "NBPF11; NBPF24", "gene_names_refseq": "NBPF11; NBPF24", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T75", "url": "https://www.uniprot.org/uniprotkb/Q86T75" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1442337066", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1442337066", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1442337066", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1442337066#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1442337066", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1442337066", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "GQDLQEQLAEGCRLAQHLVQ", "down_seq": "LSPENDNDDDEDVQVEVAEK", "snv": [ { "evidence": [ { "id": "rs1442337066", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1442337066" }, { "id": "rs1442337066", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1442337066#frequency_tab" }, { "id": "rs1442337066", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1442337066" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KLS->NLS).", "chr_id": "1", "chr_pos": "148117582", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K432", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "264", "end_pos": "264" } ] }, { "type": "snv", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "854", "end_pos": "854" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "220", "end_pos": "220" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T75-1.494.494", "start_pos": 494, "end_pos": 494, "uniprot_canonical_ac": "Q86T75-1", "length": 865, "uniprot_id": "NBPFB_HUMAN", "protein_name": "NBPF family member NBPF11", "refseq_ac": "NP_001095133", "refseq_name": "NBPF family member NBPF11 isoform b", "gene_name": "NBPF11", "gene_names_uniprotkb": "NBPF11; NBPF24", "gene_names_refseq": "NBPF11; NBPF24", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T75", "url": "https://www.uniprot.org/uniprotkb/Q86T75" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1424809642", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1424809642", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1424809642", "url": "https://www.ensembl.org/id/rs1424809642", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "SLEECAITCSNSHGPYDSNQ", "down_seq": "HRKTKITFEEDKVDSTLIGS", "snv": [ { "evidence": [ { "id": "rs1424809642", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1424809642" }, { "id": "rs1424809642", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1424809642" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NQP->NQS).", "chr_id": "1", "chr_pos": "148115898", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P494", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "264", "end_pos": "264" } ] }, { "type": "snv", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "854", "end_pos": "854" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "220", "end_pos": "220" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q86T75-1.508.508", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q86T75-1.512.512", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T75-1.508.508", "start_pos": 508, "end_pos": 508, "uniprot_canonical_ac": "Q86T75-1", "length": 865, "uniprot_id": "NBPFB_HUMAN", "protein_name": "NBPF family member NBPF11", "refseq_ac": "NP_001095133", "refseq_name": "NBPF family member NBPF11 isoform b", "gene_name": "NBPF11", "gene_names_uniprotkb": "NBPF11; NBPF24", "gene_names_refseq": "NBPF11; NBPF24", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T75", "url": "https://www.uniprot.org/uniprotkb/Q86T75" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1272701441", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1272701441", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1272701441", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1272701441", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "PYDSNQPHRKTKITFEEDKV", "down_seq": "STLIGSSSHVEWEDAVHIIP", "snv": [ { "evidence": [ { "id": "rs1272701441", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1272701441" }, { "id": "rs1272701441", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1272701441" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DST->NST).", "chr_id": "1", "chr_pos": "148115856", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D508", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "264", "end_pos": "264" } ] }, { "type": "snv", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "854", "end_pos": "854" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "220", "end_pos": "220" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q86T75-1.494.494", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q86T75-1.512.512", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T75-1.512.512", "start_pos": 512, "end_pos": 512, "uniprot_canonical_ac": "Q86T75-1", "length": 865, "uniprot_id": "NBPFB_HUMAN", "protein_name": "NBPF family member NBPF11", "refseq_ac": "NP_001095133", "refseq_name": "NBPF family member NBPF11 isoform b", "gene_name": "NBPF11", "gene_names_uniprotkb": "NBPF11; NBPF24", "gene_names_refseq": "NBPF11; NBPF24", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T75", "url": "https://www.uniprot.org/uniprotkb/Q86T75" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86T75", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86T75", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "NQPHRKTKITFEEDKVDSTL", "down_seq": "GSSSHVEWEDAVHIIPENES", "snv": [ { "evidence": [ { "id": "Q86T75", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86T75" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "I", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (IGS->NGS).", "chr_id": "1", "chr_pos": "148115843", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "I512", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "264", "end_pos": "264" } ] }, { "type": "snv", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "854", "end_pos": "854" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "220", "end_pos": "220" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q86T75-1.494.494", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q86T75-1.508.508", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T75-1.582.582", "start_pos": 582, "end_pos": 582, "uniprot_canonical_ac": "Q86T75-1", "length": 865, "uniprot_id": "NBPFB_HUMAN", "protein_name": "NBPF family member NBPF11", "refseq_ac": "NP_001095133", "refseq_name": "NBPF family member NBPF11 isoform b", "gene_name": "NBPF11", "gene_names_uniprotkb": "NBPF11; NBPF24", "gene_names_refseq": "NBPF11; NBPF24", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T75", "url": "https://www.uniprot.org/uniprotkb/Q86T75" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1258508909", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1258508909", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1258508909", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1258508909", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DEGYSTLSIPPERLASYQSY", "down_seq": "STFHSLEEQQVCMAVDIGRH", "snv": [ { "evidence": [ { "id": "rs1258508909", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1258508909" }, { "id": "rs1258508909", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1258508909" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SST->NST).", "chr_id": "1", "chr_pos": "148110434", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S582", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "264", "end_pos": "264" } ] }, { "type": "snv", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "854", "end_pos": "854" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "220", "end_pos": "220" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T75-1.650.650", "start_pos": 650, "end_pos": 650, "uniprot_canonical_ac": "Q86T75-1", "length": 865, "uniprot_id": "NBPFB_HUMAN", "protein_name": "NBPF family member NBPF11", "refseq_ac": "NP_001095133", "refseq_name": "NBPF family member NBPF11 isoform b", "gene_name": "NBPF11", "gene_names_uniprotkb": "NBPF11; NBPF24", "gene_names_refseq": "NBPF11; NBPF24", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T75", "url": "https://www.uniprot.org/uniprotkb/Q86T75" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q86T75", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86T75", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EVLQDSLDRCYSTPSVYLGL", "down_seq": "DSCQPYRSAFYVLEQQRIGL", "snv": [ { "evidence": [ { "id": "Q86T75", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q86T75" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TDS->NDS).", "chr_id": "1", "chr_pos": "148108559", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T650", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "264", "end_pos": "264" } ] }, { "type": "snv", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "854", "end_pos": "854" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "220", "end_pos": "220" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T75-1.854.854", "start_pos": 854, "end_pos": 854, "uniprot_canonical_ac": "Q86T75-1", "length": 865, "uniprot_id": "NBPFB_HUMAN", "protein_name": "NBPF family member NBPF11", "refseq_ac": "NP_001095133", "refseq_name": "NBPF family member NBPF11 isoform b", "gene_name": "NBPF11", "gene_names_uniprotkb": "NBPF11; NBPF24", "gene_names_refseq": "NBPF11; NBPF24", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T75", "url": "https://www.uniprot.org/uniprotkb/Q86T75" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1663066971", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1663066971", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1663066971", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1663066971#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "KEGEEDQRRKEEGEEKKGKK", "down_seq": "KTHHAPGSAAC", "snv": [ { "evidence": [ { "id": "rs1663066971", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1663066971" }, { "id": "rs1663066971", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1663066971#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IKT->NKT).", "chr_id": "1", "chr_pos": "148104557", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I854", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "264", "end_pos": "264" } ] }, { "type": "snv", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "854", "end_pos": "854" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "220", "end_pos": "220" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q86T75-1.220.220", "start_pos": 220, "end_pos": 220, "uniprot_canonical_ac": "Q86T75-1", "length": 865, "uniprot_id": "NBPFB_HUMAN", "protein_name": "NBPF family member NBPF11", "refseq_ac": "NP_001095133", "refseq_name": "NBPF family member NBPF11 isoform b", "gene_name": "NBPF11", "gene_names_uniprotkb": "NBPF11; NBPF24", "gene_names_refseq": "NBPF11; NBPF24", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q86T75", "url": "https://www.uniprot.org/uniprotkb/Q86T75" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Deciphering the landscape of phosphorylated HLA-II ligands.", "journal": "iScience", "date": "2022-05-20", "authors": "Solleder Marthe, Racle Julien, Guillaume Philippe, Coukos George, Bassani-Sternberg Michal, Gfeller David", "evidence": [ { "database": "iPTMnet", "id": "Q86T75", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86T75" } ], "reference": [ { "type": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ] } ], "crossref": [ { "id": "Q86T75", "url": "https://www.iedb.org/epitope/Q86T75", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q86T75", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86T75", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PEDSLEECAITCSNSHGPCD", "down_seq": "IQPHKNIKITFEEDKVNSSL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q86T75", "url": "https://www.iedb.org/epitope/Q86T75" }, { "database": "iPTMnet", "id": "Q86T75", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q86T75" }, { "database": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ], "site_lbl": "Ser220" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "264", "end_pos": "264" } ] }, { "type": "snv", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "161", "end_pos": "161" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "582", "end_pos": "582" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "854", "end_pos": "854" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "220", "end_pos": "220" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IVL0-1.1207.1207", "start_pos": 1207, "end_pos": 1207, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "database": "O-GlcNAc Atlas", "id": "Q8IVL0", "url": "https://oglcnac.org/atlas/detail/Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "database": "O-GlcNAc Atlas", "id": "Q8IVL0", "url": "https://oglcnac.org/atlas/detail/Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Ferroptosis-induced remodeling of glycosylation the immune microenvironment and improves survival in pancreatic cancer.", "journal": "World journal of surgical oncology", "date": "2025-12-05", "authors": "Tan Hao, Zhang Haitao, Gao Jiacheng, Wang Lei, Luan Xiaofeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "41350704", "url": "https://glygen.org/publication/PubMed/41350704" } ] } ], "crossref": [ { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "41350704", "url": "https://glygen.org/publication/PubMed/41350704", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IVL0", "url": "https://oglcnac.org/atlas/detail/Q8IVL0", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs2138634018", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138634018", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138634018", "url": "https://www.ensembl.org/id/rs2138634018", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2138634018", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2138634018", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1958267818", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1958267818", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1958267818", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1958267818", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs750117434", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750117434", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750117434", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750117434", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750117434", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750117434", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GRSSPVTVNQTDKEKEKVAV", "down_seq": "DSESVSLSGSPKSSPTSASA", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser1207", "evidence": [ { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "Q8IVL0", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "41350704", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/41350704" }, { "id": "Q8IVL0", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8IVL0" } ] } ], "snv": [ { "evidence": [ { "id": "rs2138634018", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138634018" }, { "id": "rs2138634018", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138634018" }, { "id": "rs2138634018", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2138634018" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->*).", "chr_id": "12", "chr_pos": "78119816", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1207", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs2138634018", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138634018" }, { "id": "rs2138634018", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138634018" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->L).", "chr_id": "12", "chr_pos": "78119816", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1207", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1958267818", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1958267818" }, { "id": "rs1958267818", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1958267818" }, { "id": "rs750117434", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750117434" }, { "id": "rs750117434", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750117434" }, { "id": "rs750117434", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750117434" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->P).", "chr_id": "12", "chr_pos": "78177198", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1207", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.1209.1209", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.1211.1211", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8IVL0-1.1219.1219", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.1226.1226", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IVL0-1.1209.1209", "start_pos": 1209, "end_pos": 1209, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "database": "O-GlcNAc Atlas", "id": "Q8IVL0", "url": "https://oglcnac.org/atlas/detail/Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "database": "O-GlcNAc Atlas", "id": "Q8IVL0", "url": "https://oglcnac.org/atlas/detail/Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Ferroptosis-induced remodeling of glycosylation the immune microenvironment and improves survival in pancreatic cancer.", "journal": "World journal of surgical oncology", "date": "2025-12-05", "authors": "Tan Hao, Zhang Haitao, Gao Jiacheng, Wang Lei, Luan Xiaofeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "41350704", "url": "https://glygen.org/publication/PubMed/41350704" } ] } ], "crossref": [ { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "41350704", "url": "https://glygen.org/publication/PubMed/41350704", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IVL0", "url": "https://oglcnac.org/atlas/detail/Q8IVL0", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs2138634390", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138634390", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138634390", "url": "https://www.ensembl.org/id/rs2138634390", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs760034299", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760034299", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760034299", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760034299", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760034299", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760034299", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs758771868", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758771868", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758771868", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758771868", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758771868", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758771868#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs758771868", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758771868", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSPVTVNQTDKEKEKVAVSD", "down_seq": "ESVSLSGSPKSSPTSASACG", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser1209", "evidence": [ { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "Q8IVL0", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "41350704", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/41350704" }, { "id": "Q8IVL0", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8IVL0" } ] } ], "snv": [ { "evidence": [ { "id": "rs2138634390", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138634390" }, { "id": "rs2138634390", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138634390" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->*).", "chr_id": "12", "chr_pos": "78119822", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1209", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760034299", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760034299" }, { "id": "rs760034299", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760034299" }, { "id": "rs760034299", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760034299" }, { "id": "rs758771868", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758771868" }, { "id": "rs758771868", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758771868" }, { "id": "rs758771868", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758771868#frequency_tab" }, { "id": "rs758771868", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758771868" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->A).", "chr_id": "12", "chr_pos": "78177204", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1209", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2138634390", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138634390" }, { "id": "rs2138634390", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138634390" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->L).", "chr_id": "12", "chr_pos": "78119822", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1209", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760034299", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760034299" }, { "id": "rs760034299", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760034299" }, { "id": "rs760034299", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760034299" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->P).", "chr_id": "12", "chr_pos": "78177204", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1209", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.1207.1207", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.1211.1211", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.1219.1219", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.1226.1226", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IVL0-1.360.360", "start_pos": 360, "end_pos": 360, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs2136562553", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136562553", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136562553", "url": "https://www.ensembl.org/id/rs2136562553", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2136562624", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136562624", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136562624", "url": "https://www.ensembl.org/id/rs2136562624", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KHSATSTMLTVKQSSTATSP", "down_seq": "PSSDRLKPPVSEGVKTAPSG", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr360", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs2136562553", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136562553" }, { "id": "rs2136562553", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136562553" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "12", "chr_pos": "78006616", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T360", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2136562624", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136562624" }, { "id": "rs2136562624", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136562624" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "12", "chr_pos": "78006617", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T360", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2136562624", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136562624" }, { "id": "rs2136562624", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136562624" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->K).", "chr_id": "12", "chr_pos": "78006617", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T360", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2136562553", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136562553" }, { "id": "rs2136562553", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136562553" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->P).", "chr_id": "12", "chr_pos": "78006616", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T360", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2136562624", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136562624" }, { "id": "rs2136562624", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136562624" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->R).", "chr_id": "12", "chr_pos": "78006617", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T360", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8IVL0-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8IVL0-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8IVL0-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.351.351", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.437.437", "start_pos": 437, "end_pos": 437, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Site-Specific Profiling of Serum Glycoproteins Using N-Linked Glycan and Glycosite Analysis Revealing Atypical N-Glycosylation Sites on Albumin and alpha-1B-Glycoprotein.", "journal": "Analytical chemistry", "date": "2018", "authors": "Sun S, Hu Y, Jia L, Eshghi ST, Liu Y, Shah P, Zhang H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "2059", "url": "https://glyconnect.expasy.org/browser/proteins/2059" } ], "reference": [ { "type": "PubMed", "id": "29671580", "url": "https://glygen.org/publication/PubMed/29671580" } ] } ], "crossref": [ { "id": "29671580", "url": "https://glygen.org/publication/PubMed/29671580", "database": "PubMed", "categories": [ "Other" ] }, { "id": "2059", "url": "https://glyconnect.expasy.org/browser/proteins/2059", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "rs2136573601", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136573601", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136573601", "url": "https://www.ensembl.org/id/rs2136573601", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2136573660", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136573660", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136573660", "url": "https://www.ensembl.org/id/rs2136573660", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1194095259", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194095259", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1194095259", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194095259", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FSESGEMEGFNSGLNSGGST", "down_seq": "SSPKVSPKLAPPKAGSKNLS", "glycosylation": [ { "glytoucan_ac": "G06356OH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn437", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "2059", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2059" } ] }, { "glytoucan_ac": "G59626AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn437", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] } ], "snv": [ { "evidence": [ { "id": "rs2136573601", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136573601" }, { "id": "rs2136573601", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136573601" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->DSS).", "chr_id": "12", "chr_pos": "78006847", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N437", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2136573601", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136573601" }, { "id": "rs2136573601", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136573601" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->HSS).", "chr_id": "12", "chr_pos": "78006847", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N437", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2136573660", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136573660" }, { "id": "rs2136573660", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136573660" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->ISS).", "chr_id": "12", "chr_pos": "78006848", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N437", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1194095259", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194095259" }, { "id": "rs1194095259", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194095259" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->KSS).", "chr_id": "12", "chr_pos": "78006849", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N437", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2136573660", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136573660" }, { "id": "rs2136573660", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136573660" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->TSS).", "chr_id": "12", "chr_pos": "78006848", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N437", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2136573601", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136573601" }, { "id": "rs2136573601", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136573601" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->YSS).", "chr_id": "12", "chr_pos": "78006847", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N437", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8IVL0-1.429.429", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.433.433", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.439.439", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8IVL0-1.440.440", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.441.441", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IVL0-1.758.758", "start_pos": 758, "end_pos": 758, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "database": "O-GlcNAc Atlas", "id": "Q8IVL0", "url": "https://oglcnac.org/atlas/detail/Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "database": "O-GlcNAc Atlas", "id": "Q8IVL0", "url": "https://oglcnac.org/atlas/detail/Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Ferroptosis-induced remodeling of glycosylation the immune microenvironment and improves survival in pancreatic cancer.", "journal": "World journal of surgical oncology", "date": "2025-12-05", "authors": "Tan Hao, Zhang Haitao, Gao Jiacheng, Wang Lei, Luan Xiaofeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "41350704", "url": "https://glygen.org/publication/PubMed/41350704" } ] } ], "crossref": [ { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "41350704", "url": "https://glygen.org/publication/PubMed/41350704", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs2137251541", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137251541", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2137251541", "url": "https://www.ensembl.org/id/rs2137251541", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2137251541", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2137251541", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TPMTWRLGQACPRLQAGDAP", "down_seq": "LGAGYPRSGTSRFIHTDPSR", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser758", "evidence": [ { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "Q8IVL0", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "41350704", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/41350704" } ] } ], "snv": [ { "evidence": [ { "id": "rs2137251541", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137251541" }, { "id": "rs2137251541", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2137251541" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->C).", "chr_id": "12", "chr_pos": "78050904", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S758", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs2137251541", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137251541" }, { "id": "rs2137251541", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2137251541" }, { "id": "rs2137251541", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2137251541" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->F).", "chr_id": "12", "chr_pos": "78050904", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S758", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->Y).", "chr_id": "12", "chr_pos": "78050904", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S758", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q8IVL0-1.753.753", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8IVL0-1.766.766", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8IVL0-1.770.770", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8IVL0-1.772.772", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IVL0-1.982.982", "start_pos": 982, "end_pos": 982, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "database": "O-GlcNAc Atlas", "id": "Q8IVL0", "url": "https://oglcnac.org/atlas/detail/Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "database": "O-GlcNAc Atlas", "id": "Q8IVL0", "url": "https://oglcnac.org/atlas/detail/Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Ferroptosis-induced remodeling of glycosylation the immune microenvironment and improves survival in pancreatic cancer.", "journal": "World journal of surgical oncology", "date": "2025-12-05", "authors": "Tan Hao, Zhang Haitao, Gao Jiacheng, Wang Lei, Luan Xiaofeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "41350704", "url": "https://glygen.org/publication/PubMed/41350704" } ] } ], "crossref": [ { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "41350704", "url": "https://glygen.org/publication/PubMed/41350704", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IVL0", "url": "https://oglcnac.org/atlas/detail/Q8IVL0", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs371371984", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371371984", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371371984", "url": "https://www.ensembl.org/id/rs371371984", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2138572300", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138572300", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138572300", "url": "https://www.ensembl.org/id/rs2138572300", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KTVSSGLPEDPEKAGQKASL", "down_seq": "VSQTGSWRRGMSAQGGAPSR", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser982", "evidence": [ { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "Q8IVL0", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "41350704", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/41350704" }, { "id": "Q8IVL0", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8IVL0" } ] } ], "snv": [ { "evidence": [ { "id": "rs371371984", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371371984" }, { "id": "rs371371984", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs371371984" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->A).", "chr_id": "12", "chr_pos": "78118201", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S982", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2138572300", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138572300" }, { "id": "rs2138572300", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138572300" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->C).", "chr_id": "12", "chr_pos": "78118202", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S982", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2138572300", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138572300" }, { "id": "rs2138572300", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138572300" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->F).", "chr_id": "12", "chr_pos": "78118202", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S982", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs371371984", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371371984" }, { "id": "rs371371984", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs371371984" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->P).", "chr_id": "12", "chr_pos": "78118201", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S982", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.978.978", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.984.984", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.988.988", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IVL0-1.984.984", "start_pos": 984, "end_pos": 984, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "database": "O-GlcNAc Atlas", "id": "Q8IVL0", "url": "https://oglcnac.org/atlas/detail/Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "database": "O-GlcNAc Atlas", "id": "Q8IVL0", "url": "https://oglcnac.org/atlas/detail/Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Ferroptosis-induced remodeling of glycosylation the immune microenvironment and improves survival in pancreatic cancer.", "journal": "World journal of surgical oncology", "date": "2025-12-05", "authors": "Tan Hao, Zhang Haitao, Gao Jiacheng, Wang Lei, Luan Xiaofeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "41350704", "url": "https://glygen.org/publication/PubMed/41350704" } ] } ], "crossref": [ { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "41350704", "url": "https://glygen.org/publication/PubMed/41350704", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IVL0", "url": "https://oglcnac.org/atlas/detail/Q8IVL0", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1005877698", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1005877698", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1005877698", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1005877698#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1005877698", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1005877698", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1005877698", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1005877698", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs778996092", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778996092", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778996092", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778996092", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778996092", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778996092", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VSSGLPEDPEKAGQKASLSV", "down_seq": "QTGSWRRGMSAQGGAPSRQK", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser984", "evidence": [ { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "Q8IVL0", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "41350704", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/41350704" }, { "id": "Q8IVL0", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8IVL0" } ] } ], "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs1005877698", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1005877698" }, { "id": "rs1005877698", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1005877698#frequency_tab" }, { "id": "rs1005877698", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1005877698" }, { "id": "rs1005877698", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1005877698" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 2 filters: num. of cancers (6); o-glyco-site-loss (S->L).", "chr_id": "12", "chr_pos": "78118208", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S984", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs1005877698", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1005877698" }, { "id": "rs1005877698", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1005877698#frequency_tab" }, { "id": "rs1005877698", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1005877698" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->*).", "chr_id": "12", "chr_pos": "78118208", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S984", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs778996092", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778996092" }, { "id": "rs778996092", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778996092" }, { "id": "rs778996092", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778996092" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->P).", "chr_id": "12", "chr_pos": "78118207", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S984", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.978.978", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.982.982", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.988.988", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IVL0-1.988.988", "start_pos": 988, "end_pos": 988, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "database": "O-GlcNAc Atlas", "id": "Q8IVL0", "url": "https://oglcnac.org/atlas/detail/Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "database": "O-GlcNAc Atlas", "id": "Q8IVL0", "url": "https://oglcnac.org/atlas/detail/Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Ferroptosis-induced remodeling of glycosylation the immune microenvironment and improves survival in pancreatic cancer.", "journal": "World journal of surgical oncology", "date": "2025-12-05", "authors": "Tan Hao, Zhang Haitao, Gao Jiacheng, Wang Lei, Luan Xiaofeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "41350704", "url": "https://glygen.org/publication/PubMed/41350704" } ] } ], "crossref": [ { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IVL0", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "41350704", "url": "https://glygen.org/publication/PubMed/41350704", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IVL0", "url": "https://oglcnac.org/atlas/detail/Q8IVL0", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1022622836", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1022622836", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1022622836", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1022622836#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1022622836", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1022622836", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LPEDPEKAGQKASLSVSQTG", "down_seq": "WRRGMSAQGGAPSRQKAGTS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser988", "evidence": [ { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "Q8IVL0", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8IVL0" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "41350704", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/41350704" }, { "id": "Q8IVL0", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8IVL0" } ] } ], "snv": [ { "evidence": [ { "id": "rs1022622836", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1022622836" }, { "id": "rs1022622836", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1022622836#frequency_tab" }, { "id": "rs1022622836", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1022622836" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->C).", "chr_id": "12", "chr_pos": "78118220", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S988", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1022622836", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1022622836" }, { "id": "rs1022622836", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1022622836#frequency_tab" }, { "id": "rs1022622836", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1022622836" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->F).", "chr_id": "12", "chr_pos": "78118220", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S988", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1022622836", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1022622836" }, { "id": "rs1022622836", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1022622836#frequency_tab" }, { "id": "rs1022622836", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1022622836" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->Y).", "chr_id": "12", "chr_pos": "78118220", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S988", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.978.978", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.982.982", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.984.984", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IVL0-1.333.333", "start_pos": 333, "end_pos": 333, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "STAGQPPASAIPSPSASKPW", "down_seq": "SKSMNVKHSATSTMLTVKQS", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 2 filters: patient freq. (1.1%); num. of cancers (3).", "chr_id": "12", "chr_pos": "78006536", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R333", "keywords": [ "biomuta", "somatic", "cancer", "disease" ], "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8IVL0-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8IVL0-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8IVL0-1.351.351", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.872.872", "start_pos": 872, "end_pos": 872, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs751418701", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751418701", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751418701", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751418701", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751418701", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751418701#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs751418701", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751418701", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs751418701", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs751418701", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1883933075", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1883933075", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1883933075", "url": "https://www.ensembl.org/id/rs1883933075", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SLNRIPDTATSRDIIQRGVH", "down_seq": "VTVDADSWDDSSSVSSGLSD", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs751418701", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751418701" }, { "id": "rs751418701", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751418701" }, { "id": "rs751418701", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751418701#frequency_tab" }, { "id": "rs751418701", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751418701" }, { "id": "rs751418701", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs751418701" }, { "id": "rs1883933075", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1883933075" }, { "id": "rs1883933075", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1883933075" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); n-glyco-sequon-gain (DVT->NVT).", "chr_id": "12", "chr_pos": "78059093", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D872", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid cancer", "description": "An endocrine gland cancer located in the thyroid gland located in the neck below the thyroid cartilage." }, "synonyms": [ { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "Thyroid gland neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant tumour of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid gland cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3973", "DOID:0080524", "DOID:0080525" ], "evidence": [ { "id": "1781", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1781" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.881.881", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.882.882", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8IVL0-1.883.883", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1020.1020", "start_pos": 1020, "end_pos": 1020, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1215026389", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1215026389", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1215026389", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1215026389#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1215026389", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1215026389", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PSRQKAGTSALKTPGKTDDA", "down_seq": "ASEKGKAPLKGSSLQRSPSD", "snv": [ { "evidence": [ { "id": "rs1215026389", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1215026389" }, { "id": "rs1215026389", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1215026389#frequency_tab" }, { "id": "rs1215026389", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1215026389" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KAS->NAS).", "chr_id": "12", "chr_pos": "78119256", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1020", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.1030.1030", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1030.1030", "start_pos": 1030, "end_pos": 1030, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs534756307", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534756307", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs534756307", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs534756307", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs534756307", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534756307", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs534756307", "url": "http://gnomad.broadinstitute.org/awesome?query=rs534756307", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LKTPGKTDDAKASEKGKAPL", "down_seq": "GSSLQRSPSDAGKSSGDEGK", "snv": [ { "evidence": [ { "id": "rs534756307", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534756307" }, { "id": "rs534756307", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs534756307" }, { "id": "rs534756307", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534756307" }, { "id": "rs534756307", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs534756307" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KGS->NGS).", "chr_id": "12", "chr_pos": "78119286", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1030", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.1020.1020", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.1043.1043", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1043.1043", "start_pos": 1043, "end_pos": 1043, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138603515", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138603515", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138603515", "url": "https://www.ensembl.org/id/rs2138603515", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "EKGKAPLKGSSLQRSPSDAG", "down_seq": "SSGDEGKKPPSGIGRSTATS", "snv": [ { "evidence": [ { "id": "rs2138603515", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138603515" }, { "id": "rs2138603515", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138603515" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KSS->NSS).", "chr_id": "12", "chr_pos": "78119325", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1043", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.1030.1030", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.1060.1060", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.1062.1062", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1060.1060", "start_pos": 1060, "end_pos": 1060, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DAGKSSGDEGKKPPSGIGRS", "down_seq": "ATSSFGFKKPSGVGSSAMIT", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TAT->NAT).", "chr_id": "12", "chr_pos": "78119375", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T1060", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.1043.1043", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.1062.1062", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.1079.1079", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8IVL0-1.1080.1080", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1062.1062", "start_pos": 1062, "end_pos": 1062, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2138606865", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138606865", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138606865", "url": "https://www.ensembl.org/id/rs2138606865", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2138606865", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2138606865", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GKSSGDEGKKPPSGIGRSTA", "down_seq": "SSFGFKKPSGVGSSAMITSS", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs2138606865", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138606865" }, { "id": "rs2138606865", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138606865" }, { "id": "rs2138606865", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2138606865" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TSS->NSS).", "chr_id": "12", "chr_pos": "78119381", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T1062", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.1043.1043", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.1060.1060", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.1079.1079", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8IVL0-1.1080.1080", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1079.1079", "start_pos": 1079, "end_pos": 1079, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138610187", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138610187", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138610187", "url": "https://www.ensembl.org/id/rs2138610187", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "STATSSFGFKKPSGVGSSAM", "down_seq": "TSSGATITSGSATLGKIPKS", "snv": [ { "evidence": [ { "id": "rs2138610187", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138610187" }, { "id": "rs2138610187", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138610187" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (ITS->NTS).", "chr_id": "12", "chr_pos": "78119432", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1079", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.1060.1060", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.1062.1062", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.1080.1080", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.1085.1085", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.1088.1088", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1080.1080", "start_pos": 1080, "end_pos": 1080, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1955569380", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1955569380", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1955569380", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1955569380#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TATSSFGFKKPSGVGSSAMI", "down_seq": "SSGATITSGSATLGKIPKSA", "snv": [ { "evidence": [ { "id": "rs1955569380", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1955569380" }, { "id": "rs1955569380", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1955569380#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TSS->NSS).", "chr_id": "12", "chr_pos": "78119435", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1080", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8IVL0-1.1060.1060", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8IVL0-1.1062.1062", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.1079.1079", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8IVL0-1.1085.1085", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8IVL0-1.1088.1088", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8IVL0-1.1100.1100", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1085.1085", "start_pos": 1085, "end_pos": 1085, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs746964202", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746964202", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746964202", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746964202", "database": "ExAC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "FGFKKPSGVGSSAMITSSGA", "down_seq": "ITSGSATLGKIPKSAAIGGK", "snv": [ { "evidence": [ { "id": "rs746964202", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746964202" }, { "id": "rs746964202", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746964202" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TIT->NIT).", "chr_id": "12", "chr_pos": "78119450", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1085", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.1079.1079", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8IVL0-1.1080.1080", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8IVL0-1.1088.1088", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.1100.1100", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1088.1088", "start_pos": 1088, "end_pos": 1088, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2138611980", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138611980", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138611980", "url": "https://www.ensembl.org/id/rs2138611980", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2138611980", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2138611980", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KKPSGVGSSAMITSSGATIT", "down_seq": "GSATLGKIPKSAAIGGKSNA", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs2138611980", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138611980" }, { "id": "rs2138611980", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138611980" }, { "id": "rs2138611980", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2138611980" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SGS->NGS).", "chr_id": "12", "chr_pos": "78119459", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1088", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.1079.1079", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8IVL0-1.1080.1080", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8IVL0-1.1085.1085", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8IVL0-1.1100.1100", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1100.1100", "start_pos": 1100, "end_pos": 1100, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TSSGATITSGSATLGKIPKS", "down_seq": "AIGGKSNAGRKTSLDGSQNQ", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78119494", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A1100", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8IVL0-1.1080.1080", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.1085.1085", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8IVL0-1.1088.1088", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8IVL0-1.1111.1111", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.1115.1115", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1111.1111", "start_pos": 1111, "end_pos": 1111, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138616433", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138616433", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138616433", "url": "https://www.ensembl.org/id/rs2138616433", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ATLGKIPKSAAIGGKSNAGR", "down_seq": "TSLDGSQNQDDVVLHVSSKT", "snv": [ { "evidence": [ { "id": "rs2138616433", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138616433" }, { "id": "rs2138616433", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138616433" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KTS->NTS).", "chr_id": "12", "chr_pos": "78119529", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1111", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8IVL0-1.1100.1100", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.1115.1115", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.1130.1130", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1115.1115", "start_pos": 1115, "end_pos": 1115, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138616955", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138616955", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138616955", "url": "https://www.ensembl.org/id/rs2138616955", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KIPKSAAIGGKSNAGRKTSL", "down_seq": "GSQNQDDVVLHVSSKTTLQY", "snv": [ { "evidence": [ { "id": "rs2138616955", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138616955" }, { "id": "rs2138616955", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138616955" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DGS->NGS).", "chr_id": "12", "chr_pos": "78119539", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1115", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.1100.1100", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.1111.1111", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.1130.1130", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8IVL0-1.1135.1135", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1130.1130", "start_pos": 1130, "end_pos": 1130, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138619934", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138619934", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138619934", "url": "https://www.ensembl.org/id/rs2138619934", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2138619934", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2138619934", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "RKTSLDGSQNQDDVVLHVSS", "down_seq": "TTLQYRSLPRPSKSSTSGIP", "snv": [ { "evidence": [ { "id": "rs2138619934", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138619934" }, { "id": "rs2138619934", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138619934" }, { "id": "rs2138619934", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2138619934" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KTT->NTT).", "chr_id": "NC_000012.12", "chr_pos": "78119586", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K1130", "keywords": [ "ebi", "somatic", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.1111.1111", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.1115.1115", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8IVL0-1.1135.1135", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.1143.1143", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.1145.1145", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1135.1135", "start_pos": 1135, "end_pos": 1135, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138620761", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138620761", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138620761", "url": "https://www.ensembl.org/id/rs2138620761", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DGSQNQDDVVLHVSSKTTLQ", "down_seq": "RSLPRPSKSSTSGIPGRGGH", "snv": [ { "evidence": [ { "id": "rs2138620761", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138620761" }, { "id": "rs2138620761", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138620761" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YRS->NRS).", "chr_id": "12", "chr_pos": "78119599", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1135", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8IVL0-1.1115.1115", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8IVL0-1.1130.1130", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8IVL0-1.1143.1143", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.1145.1145", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1143.1143", "start_pos": 1143, "end_pos": 1143, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138622373", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138622373", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138622373", "url": "https://www.ensembl.org/id/rs2138622373", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VVLHVSSKTTLQYRSLPRPS", "down_seq": "SSTSGIPGRGGHRSSTSSID", "snv": [ { "evidence": [ { "id": "rs2138622373", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138622373" }, { "id": "rs2138622373", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138622373" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KSS->NSS).", "chr_id": "12", "chr_pos": "78119625", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1143", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.1130.1130", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8IVL0-1.1135.1135", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.1145.1145", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.1158.1158", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8IVL0-1.1159.1159", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.1162.1162", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1145.1145", "start_pos": 1145, "end_pos": 1145, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs776848725", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776848725", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776848725", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776848725", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776848725", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776848725#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs776848725", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776848725", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LHVSSKTTLQYRSLPRPSKS", "down_seq": "TSGIPGRGGHRSSTSSIDSN", "snv": [ { "evidence": [ { "id": "rs776848725", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776848725" }, { "id": "rs776848725", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776848725" }, { "id": "rs776848725", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776848725#frequency_tab" }, { "id": "rs776848725", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776848725" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (STS->NTS).", "chr_id": "12", "chr_pos": "78119630", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1145", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.1130.1130", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.1135.1135", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.1143.1143", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.1158.1158", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8IVL0-1.1159.1159", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.1162.1162", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1158.1158", "start_pos": 1158, "end_pos": 1158, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2139648247", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139648247", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2139648247", "url": "https://www.ensembl.org/id/rs2139648247", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs752134011", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752134011", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752134011", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752134011", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752134011", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752134011#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs752134011", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752134011", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LPRPSKSSTSGIPGRGGHRS", "down_seq": "TSSIDSNVSSKSAGATTSKL", "snv": [ { "evidence": [ { "id": "rs2139648247", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139648247" }, { "id": "rs2139648247", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2139648247" }, { "id": "rs752134011", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752134011" }, { "id": "rs752134011", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752134011" }, { "id": "rs752134011", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs752134011#frequency_tab" }, { "id": "rs752134011", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752134011" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (STS->NTS).", "chr_id": "12", "chr_pos": "78175339", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1158", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.1143.1143", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.1145.1145", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.1159.1159", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.1162.1162", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.1168.1168", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8IVL0-1.1174.1174", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1159.1159", "start_pos": 1159, "end_pos": 1159, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1268121136", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1268121136", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1268121136", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1268121136", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PRPSKSSTSGIPGRGGHRSS", "down_seq": "SSIDSNVSSKSAGATTSKLR", "snv": [ { "evidence": [ { "id": "rs1268121136", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1268121136" }, { "id": "rs1268121136", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1268121136" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TSS->NSS).", "chr_id": "12", "chr_pos": "78119672", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1159", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8IVL0-1.1143.1143", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8IVL0-1.1145.1145", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.1158.1158", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8IVL0-1.1162.1162", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.1168.1168", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.1174.1174", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1162.1162", "start_pos": 1162, "end_pos": 1162, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs61754963", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61754963", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs61754963", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61754963", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs61754963", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61754963", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs61754963", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61754963#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs61754963", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61754963", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2138625990", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138625990", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138625990", "url": "https://www.ensembl.org/id/rs2138625990", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "SKSSTSGIPGRGGHRSSTSS", "down_seq": "DSNVSSKSAGATTSKLREPT", "snv": [ { "evidence": [ { "id": "rs61754963", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61754963" }, { "id": "rs61754963", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61754963" }, { "id": "rs61754963", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61754963" }, { "id": "rs61754963", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61754963#frequency_tab" }, { "id": "rs61754963", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61754963" }, { "id": "rs2138625990", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138625990" }, { "id": "rs2138625990", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138625990" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IDS->NDS).", "chr_id": "12", "chr_pos": "78175351", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1162", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.1143.1143", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.1145.1145", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.1158.1158", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8IVL0-1.1159.1159", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.1168.1168", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8IVL0-1.1174.1174", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1168.1168", "start_pos": 1168, "end_pos": 1168, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs954349494", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs954349494", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs954349494", "url": "https://www.ensembl.org/id/rs954349494", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs954349494", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs954349494", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GIPGRGGHRSSTSSIDSNVS", "down_seq": "KSAGATTSKLREPTKIGSGR", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs954349494", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs954349494" }, { "id": "rs954349494", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs954349494" }, { "id": "rs954349494", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs954349494" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SKS->NKS).", "chr_id": "12", "chr_pos": "78119699", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1168", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.1158.1158", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.1159.1159", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.1162.1162", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.1174.1174", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8IVL0-1.1184.1184", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1174.1174", "start_pos": 1174, "end_pos": 1174, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138628259", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138628259", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138628259", "url": "https://www.ensembl.org/id/rs2138628259", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GHRSSTSSIDSNVSSKSAGA", "down_seq": "TSKLREPTKIGSGRSSPVTV", "snv": [ { "evidence": [ { "id": "rs2138628259", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138628259" }, { "id": "rs2138628259", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138628259" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TTS->NTS).", "chr_id": "12", "chr_pos": "78119717", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1174", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8IVL0-1.1158.1158", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.1159.1159", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8IVL0-1.1162.1162", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.1168.1168", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.1184.1184", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1184.1184", "start_pos": 1184, "end_pos": 1184, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs770038391", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770038391", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770038391", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770038391", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs770038391", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770038391", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "SNVSSKSAGATTSKLREPTK", "down_seq": "GSGRSSPVTVNQTDKEKEKV", "snv": [ { "evidence": [ { "id": "rs770038391", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770038391" }, { "id": "rs770038391", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770038391" }, { "id": "rs770038391", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770038391" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IGS->NGS).", "chr_id": "12", "chr_pos": "78119747", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1184", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8IVL0-1.1168.1168", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.1174.1174", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1211.1211", "start_pos": 1211, "end_pos": 1211, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138634769", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138634769", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138634769", "url": "https://www.ensembl.org/id/rs2138634769", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2138634769", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2138634769", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PVTVNQTDKEKEKVAVSDSE", "down_seq": "VSLSGSPKSSPTSASACGAQ", "snv": [ { "evidence": [ { "id": "rs2138634769", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138634769" }, { "id": "rs2138634769", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138634769" }, { "id": "rs2138634769", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2138634769" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SVS->NVS).", "chr_id": "12", "chr_pos": "78119828", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1211", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.1207.1207", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.1209.1209", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8IVL0-1.1219.1219", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.1226.1226", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1219.1219", "start_pos": 1219, "end_pos": 1219, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138636279", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138636279", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138636279", "url": "https://www.ensembl.org/id/rs2138636279", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KEKEKVAVSDSESVSLSGSP", "down_seq": "SSPTSASACGAQGLRQPGSK", "snv": [ { "evidence": [ { "id": "rs2138636279", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138636279" }, { "id": "rs2138636279", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138636279" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KSS->NSS).", "chr_id": "12", "chr_pos": "78119853", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1219", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8IVL0-1.1207.1207", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.1209.1209", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8IVL0-1.1211.1211", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8IVL0-1.1226.1226", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1226.1226", "start_pos": 1226, "end_pos": 1226, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs530741171", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs530741171", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs530741171", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs530741171", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs530741171", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs530741171", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs530741171", "url": "http://gnomad.broadinstitute.org/awesome?query=rs530741171", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VSDSESVSLSGSPKSSPTSA", "down_seq": "ACGAQGLRQPGSKYPDIASP", "snv": [ { "evidence": [ { "id": "rs530741171", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs530741171" }, { "id": "rs530741171", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs530741171" }, { "id": "rs530741171", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs530741171" }, { "id": "rs530741171", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs530741171" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SAC->NAC).", "chr_id": "12", "chr_pos": "78119873", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "S1226", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.1207.1207", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.1209.1209", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.1211.1211", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8IVL0-1.1219.1219", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.1243.1243", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1243.1243", "start_pos": 1243, "end_pos": 1243, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1955597149", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1955597149", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1955597149", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1955597149#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "TSASACGAQGLRQPGSKYPD", "down_seq": "ASPTFRRLFGAKAGGKSASA", "snv": [ { "evidence": [ { "id": "rs1955597149", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1955597149" }, { "id": "rs1955597149", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1955597149#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IAS->NAS).", "chr_id": "12", "chr_pos": "78119924", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1243", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.1226.1226", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.1249.1249", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1249.1249", "start_pos": 1249, "end_pos": 1249, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GAQGLRQPGSKYPDIASPTF", "down_seq": "RLFGAKAGGKSASAPNTEGV", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "12", "chr_pos": "78119941", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1249", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "12", "chr_pos": "78119942", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1249", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.1243.1243", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1270.1270", "start_pos": 1270, "end_pos": 1270, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1027186620", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1027186620", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1027186620", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1027186620#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "RLFGAKAGGKSASAPNTEGV", "down_seq": "SSSVMPSPSTTLARQGSLES", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs1027186620", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1027186620" }, { "id": "rs1027186620", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1027186620#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KSS->NSS).", "chr_id": "12", "chr_pos": "78122000", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K1270", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.1279.1279", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.1283.1283", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1279.1279", "start_pos": 1279, "end_pos": 1279, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1350893796", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1350893796", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1350893796", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1350893796#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1350893796", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1350893796", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1350893796", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1350893796", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KSASAPNTEGVKSSSVMPSP", "down_seq": "TTLARQGSLESPSSGTGSMG", "snv": [ { "evidence": [ { "id": "rs1350893796", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1350893796" }, { "id": "rs1350893796", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1350893796#frequency_tab" }, { "id": "rs1350893796", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1350893796" }, { "id": "rs1350893796", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1350893796" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (STT->NTT).", "chr_id": "12", "chr_pos": "78122026", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1279", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.1270.1270", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.1283.1283", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1283.1283", "start_pos": 1283, "end_pos": 1283, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "APNTEGVKSSSVMPSPSTTL", "down_seq": "RQGSLESPSSGTGSMGSAGG", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78122038", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A1283", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.1270.1270", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.1279.1279", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1305.1305", "start_pos": 1305, "end_pos": 1305, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138687907", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138687907", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138687907", "url": "https://www.ensembl.org/id/rs2138687907", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QGSLESPSSGTGSMGSAGGL", "down_seq": "GSSSPLFNKPSDLTTDVISL", "snv": [ { "evidence": [ { "id": "rs2138687907", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138687907" }, { "id": "rs2138687907", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138687907" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SGS->NGS).", "chr_id": "12", "chr_pos": "78122104", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1305", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.1307.1307", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.1315.1315", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8IVL0-1.1317.1317", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.1324.1324", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1307.1307", "start_pos": 1307, "end_pos": 1307, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138688331", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138688331", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138688331", "url": "https://www.ensembl.org/id/rs2138688331", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SLESPSSGTGSMGSAGGLSG", "down_seq": "SSPLFNKPSDLTTDVISLSH", "snv": [ { "evidence": [ { "id": "rs2138688331", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138688331" }, { "id": "rs2138688331", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138688331" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SSS->NSS).", "chr_id": "12", "chr_pos": "78122110", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1307", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.1305.1305", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8IVL0-1.1315.1315", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.1317.1317", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.1324.1324", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.1326.1326", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1315.1315", "start_pos": 1315, "end_pos": 1315, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs779085012", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779085012", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779085012", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779085012", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779085012", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779085012#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779085012", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779085012", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "TGSMGSAGGLSGSSSPLFNK", "down_seq": "SDLTTDVISLSHSLASSPAS", "snv": [ { "evidence": [ { "id": "rs779085012", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779085012" }, { "id": "rs779085012", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779085012" }, { "id": "rs779085012", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779085012#frequency_tab" }, { "id": "rs779085012", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779085012" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKP->NKS).", "chr_id": "12", "chr_pos": "78122133", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1315", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs779085012", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779085012" }, { "id": "rs779085012", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779085012" }, { "id": "rs779085012", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779085012#frequency_tab" }, { "id": "rs779085012", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779085012" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKP->NKT).", "chr_id": "12", "chr_pos": "78122133", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1315", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.1305.1305", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8IVL0-1.1307.1307", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.1317.1317", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.1324.1324", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8IVL0-1.1326.1326", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8IVL0-1.1333.1333", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1317.1317", "start_pos": 1317, "end_pos": 1317, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138690116", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138690116", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138690116", "url": "https://www.ensembl.org/id/rs2138690116", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SMGSAGGLSGSSSPLFNKPS", "down_seq": "LTTDVISLSHSLASSPASVH", "snv": [ { "evidence": [ { "id": "rs2138690116", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138690116" }, { "id": "rs2138690116", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138690116" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DLT->NLT).", "chr_id": "12", "chr_pos": "78122139", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1317", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8IVL0-1.1305.1305", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.1307.1307", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.1315.1315", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8IVL0-1.1324.1324", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.1326.1326", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8IVL0-1.1333.1333", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1324.1324", "start_pos": 1324, "end_pos": 1324, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138691520", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138691520", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138691520", "url": "https://www.ensembl.org/id/rs2138691520", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LSGSSSPLFNKPSDLTTDVI", "down_seq": "LSHSLASSPASVHSFTSGGL", "snv": [ { "evidence": [ { "id": "rs2138691520", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138691520" }, { "id": "rs2138691520", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138691520" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SLS->NLS).", "chr_id": "12", "chr_pos": "78122161", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1324", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.1305.1305", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.1307.1307", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.1315.1315", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8IVL0-1.1317.1317", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.1326.1326", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.1333.1333", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1326.1326", "start_pos": 1326, "end_pos": 1326, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1955699434", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1955699434", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1955699434", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1955699434#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GSSSPLFNKPSDLTTDVISL", "down_seq": "HSLASSPASVHSFTSGGLVW", "snv": [ { "evidence": [ { "id": "rs1955699434", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1955699434" }, { "id": "rs1955699434", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1955699434#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SHS->NHS).", "chr_id": "12", "chr_pos": "78122167", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1326", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.1307.1307", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8IVL0-1.1315.1315", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.1317.1317", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.1324.1324", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8IVL0-1.1333.1333", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1333.1333", "start_pos": 1333, "end_pos": 1333, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "NKPSDLTTDVISLSHSLASS", "down_seq": "ASVHSFTSGGLVWAANMSSS", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "12", "chr_pos": "78122187", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P1333", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8IVL0-1.1315.1315", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8IVL0-1.1317.1317", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.1324.1324", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8IVL0-1.1326.1326", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8IVL0-1.1351.1351", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.1352.1352", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.134.134", "start_pos": 134, "end_pos": 134, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2137485008", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137485008", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2137485008", "url": "https://www.ensembl.org/id/rs2137485008", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AEIIQIIANEKVEDINGCPR", "down_seq": "QSQMIENVDVCLSFLAARGV", "snv": [ { "evidence": [ { "id": "rs2137485008", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137485008" }, { "id": "rs2137485008", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2137485008" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SQS->NQS).", "chr_id": "12", "chr_pos": "77941120", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S134", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1351.1351", "start_pos": 1351, "end_pos": 1351, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs762407432", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762407432", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762407432", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762407432", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762407432", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762407432", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs762407432", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs762407432", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSPASVHSFTSGGLVWAANM", "down_seq": "SSSAGSKDTPSYQSMTSLHT", "snv": [ { "evidence": [ { "id": "rs762407432", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762407432" }, { "id": "rs762407432", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762407432" }, { "id": "rs762407432", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762407432" }, { "id": "rs762407432", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs762407432" } ], "glycoeffect": [ "n-glyco-sequon-gain", "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SSS->NSS).", "chr_id": "12", "chr_pos": "78122242", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1351", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8IVL0-1.1333.1333", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.1352.1352", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8IVL0-1.1358.1358", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8IVL0-1.1363.1363", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1352.1352", "start_pos": 1352, "end_pos": 1352, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1955704149", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1955704149", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1955704149", "url": "https://www.ensembl.org/id/rs1955704149", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPASVHSFTSGGLVWAANMS", "down_seq": "SSAGSKDTPSYQSMTSLHTS", "snv": [ { "evidence": [ { "id": "rs1955704149", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1955704149" }, { "id": "rs1955704149", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1955704149" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SSS->NSS).", "chr_id": "12", "chr_pos": "78122245", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1352", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.1333.1333", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.1351.1351", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.1358.1358", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8IVL0-1.1363.1363", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1358.1358", "start_pos": 1358, "end_pos": 1358, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138697804", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138697804", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138697804", "url": "https://www.ensembl.org/id/rs2138697804", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SFTSGGLVWAANMSSSSAGS", "down_seq": "DTPSYQSMTSLHTSSESIDL", "snv": [ { "evidence": [ { "id": "rs2138697804", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138697804" }, { "id": "rs2138697804", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138697804" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KDT->NDT).", "chr_id": "12", "chr_pos": "78122264", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1358", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q8IVL0-1.1351.1351", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.1352.1352", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8IVL0-1.1363.1363", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1363.1363", "start_pos": 1363, "end_pos": 1363, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138698750", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138698750", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138698750", "url": "https://www.ensembl.org/id/rs2138698750", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "GLVWAANMSSSSAGSKDTPS", "down_seq": "QSMTSLHTSSESIDLPLSHH", "snv": [ { "evidence": [ { "id": "rs2138698750", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138698750" }, { "id": "rs2138698750", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138698750" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YQS->NQS).", "chr_id": "12", "chr_pos": "78122277", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1363", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8IVL0-1.1351.1351", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8IVL0-1.1352.1352", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8IVL0-1.1358.1358", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8IVL0-1.1383.1383", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1383.1383", "start_pos": 1383, "end_pos": 1383, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1955709708", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1955709708", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1955709708", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1955709708#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "YQSMTSLHTSSESIDLPLSH", "down_seq": "GSLSGLTTGTHEVQSLLMRT", "snv": [ { "evidence": [ { "id": "rs1955709708", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1955709708" }, { "id": "rs1955709708", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1955709708#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HGS->NGS).", "chr_id": "12", "chr_pos": "78122337", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1383", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8IVL0-1.1363.1363", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.1392.1392", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8IVL0-1.1403.1403", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1392.1392", "start_pos": 1392, "end_pos": 1392, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SSESIDLPLSHHGSLSGLTT", "down_seq": "THEVQSLLMRTGSVRSTLSE", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78122365", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G1392", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.1383.1383", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8IVL0-1.1403.1403", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.1409.1409", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1403.1403", "start_pos": 1403, "end_pos": 1403, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HGSLSGLTTGTHEVQSLLMR", "down_seq": "GSVRSTLSESMQLDRNTLPK", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "12", "chr_pos": "78122398", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T1403", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8IVL0-1.1383.1383", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8IVL0-1.1392.1392", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.1409.1409", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1409.1409", "start_pos": 1409, "end_pos": 1409, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs778854137", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778854137", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778854137", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778854137", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778854137", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778854137#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs778854137", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778854137", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs778854137", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs778854137", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LTTGTHEVQSLLMRTGSVRS", "down_seq": "LSESMQLDRNTLPKKGLRYT", "snv": [ { "evidence": [ { "id": "rs778854137", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778854137" }, { "id": "rs778854137", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778854137" }, { "id": "rs778854137", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778854137#frequency_tab" }, { "id": "rs778854137", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778854137" }, { "id": "rs778854137", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs778854137" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TLS->NLS).", "chr_id": "12", "chr_pos": "78122416", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1409", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.1392.1392", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.1403.1403", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1447.1447", "start_pos": 1447, "end_pos": 1447, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1376075236", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1376075236", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1376075236", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1376075236#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1376075236", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1376075236", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "RYTPSSRQANQEEGKEWLRS", "down_seq": "STGGLQDTGNQSPLVSPSAM", "snv": [ { "evidence": [ { "id": "rs1376075236", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1376075236" }, { "id": "rs1376075236", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1376075236#frequency_tab" }, { "id": "rs1376075236", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1376075236" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HST->NST).", "chr_id": "12", "chr_pos": "78128764", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1447", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q8IVL0-1.1459.1459", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8IVL0-1.1463.1463", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1476.1476", "start_pos": 1476, "end_pos": 1476, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1467135677", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1467135677", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1467135677", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1467135677#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1467135677", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1467135677", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "GNQSPLVSPSAMSSSAAGKY", "down_seq": "FSNLVSPTNLSQFNLPGPSM", "snv": [ { "evidence": [ { "id": "rs1467135677", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1467135677" }, { "id": "rs1467135677", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1467135677#frequency_tab" }, { "id": "rs1467135677", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1467135677" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HFS->NFS).", "chr_id": "12", "chr_pos": "78128851", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1476", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.1459.1459", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.1463.1463", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8IVL0-1.1492.1492", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.1493.1493", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.1495.1495", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1492.1492", "start_pos": 1492, "end_pos": 1492, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1166094251", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1166094251", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1166094251", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1166094251", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "AGKYHFSNLVSPTNLSQFNL", "down_seq": "GPSMMRSNSIPAQDSSFDLY", "snv": [ { "evidence": [ { "id": "rs1166094251", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1166094251" }, { "id": "rs1166094251", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1166094251" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLP->NLS).", "chr_id": "12", "chr_pos": "78137209", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1492", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8IVL0-1.1476.1476", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.1493.1493", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8IVL0-1.1495.1495", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8IVL0-1.1510.1510", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1493.1493", "start_pos": 1493, "end_pos": 1493, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GKYHFSNLVSPTNLSQFNLP", "down_seq": "PSMMRSNSIPAQDSSFDLYD", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "12", "chr_pos": "78137212", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "G1493", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.1476.1476", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.1492.1492", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.1495.1495", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.1510.1510", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1495.1495", "start_pos": 1495, "end_pos": 1495, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YHFSNLVSPTNLSQFNLPGP", "down_seq": "MMRSNSIPAQDSSFDLYDDS", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78137218", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S1495", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.1476.1476", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8IVL0-1.1492.1492", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.1493.1493", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.1510.1510", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1510.1510", "start_pos": 1510, "end_pos": 1510, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "NLPGPSMMRSNSIPAQDSSF", "down_seq": "LYDDSQLCGSATSLEERPRA", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78137263", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "D1510", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8IVL0-1.1492.1492", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.1493.1493", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.1495.1495", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1534.1534", "start_pos": 1534, "end_pos": 1534, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DSQLCGSATSLEERPRAISH", "down_seq": "GSFRDSMEEVHGSSLSLVSS", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78137336", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S1534", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "Q8IVL0-1.1554.1554", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1554.1554", "start_pos": 1554, "end_pos": 1554, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2139065591", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139065591", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2139065591", "url": "https://www.ensembl.org/id/rs2139065591", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2139065591", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2139065591", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SGSFRDSMEEVHGSSLSLVS", "down_seq": "TSSLYSTAEEKAHSEQIHKL", "snv": [ { "evidence": [ { "id": "rs2139065591", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139065591" }, { "id": "rs2139065591", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2139065591" }, { "id": "rs2139065591", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2139065591" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (STS->NTS).", "chr_id": "12", "chr_pos": "78140312", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1554", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8IVL0-1.1534.1534", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8IVL0-1.1559.1559", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.1564.1564", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1559.1559", "start_pos": 1559, "end_pos": 1559, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2139066086", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139066086", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2139066086", "url": "https://www.ensembl.org/id/rs2139066086", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DSMEEVHGSSLSLVSSTSSL", "down_seq": "STAEEKAHSEQIHKLRRELV", "snv": [ { "evidence": [ { "id": "rs2139066086", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139066086" }, { "id": "rs2139066086", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2139066086" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YST->NST).", "chr_id": "12", "chr_pos": "78140326", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y1559", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q8IVL0-1.1554.1554", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8IVL0-1.1564.1564", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8IVL0-1.1575.1575", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1564.1564", "start_pos": 1564, "end_pos": 1564, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "VHGSSLSLVSSTSSLYSTAE", "down_seq": "KAHSEQIHKLRRELVASQEK", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78146375", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E1564", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.1554.1554", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8IVL0-1.1559.1559", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8IVL0-1.1575.1575", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1575.1575", "start_pos": 1575, "end_pos": 1575, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TSSLYSTAEEKAHSEQIHKL", "down_seq": "RELVASQEKVATLTSQLSAN", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78148857", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1575", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8IVL0-1.1559.1559", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8IVL0-1.1564.1564", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8IVL0-1.1587.1587", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1587.1587", "start_pos": 1587, "end_pos": 1587, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs766762443", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766762443", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs766762443", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766762443", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs766762443", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766762443", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HSEQIHKLRRELVASQEKVA", "down_seq": "LTSQLSANAHLVAAFEKSLG", "snv": [ { "evidence": [ { "id": "rs766762443", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766762443" }, { "id": "rs766762443", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766762443" }, { "id": "rs766762443", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766762443" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TLT->NLT).", "chr_id": "12", "chr_pos": "78148894", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1587", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8IVL0-1.1575.1575", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1612.1612", "start_pos": 1612, "end_pos": 1612, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LSANAHLVAAFEKSLGNMTG", "down_seq": "LQSLTMTAEQKESELIELRE", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78159252", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1612", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q8IVL0-1.1615.1615", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1615.1615", "start_pos": 1615, "end_pos": 1615, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NAHLVAAFEKSLGNMTGRLQ", "down_seq": "LTMTAEQKESELIELRETIE", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SLT->NLT).", "chr_id": "12", "chr_pos": "78159261", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1615", "disease": [ { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q8IVL0-1.1612.1612", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1655.1655", "start_pos": 1655, "end_pos": 1655, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs866321098", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs866321098", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs866321098", "url": "https://www.ensembl.org/id/rs866321098", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "EMLKAQNSAAQAAIQGALNG", "down_seq": "DHPPKDLRIRRQHSSESVSS", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs866321098", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs866321098" }, { "id": "rs866321098", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs866321098" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NGP->NGS).", "chr_id": "12", "chr_pos": "78168848", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P1655", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q8IVL0-1.1663.1663", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.1668.1668", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.1672.1672", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1663.1663", "start_pos": 1663, "end_pos": 1663, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AAQAAIQGALNGPDHPPKDL", "down_seq": "IRRQHSSESVSSINSATSHS", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "12", "chr_pos": "78175312", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1663", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8IVL0-1.1655.1655", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8IVL0-1.1668.1668", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.1672.1672", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.1676.1676", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.1678.1678", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8IVL0-1.1679.1679", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.1682.1682", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1668.1668", "start_pos": 1668, "end_pos": 1668, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1219195597", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1219195597", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1219195597", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1219195597#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1219195597", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1219195597", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "IQGALNGPDHPPKDLRIRRQ", "down_seq": "SSESVSSINSATSHSSIGSG", "snv": [ { "evidence": [ { "id": "rs1219195597", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1219195597" }, { "id": "rs1219195597", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1219195597#frequency_tab" }, { "id": "rs1219195597", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1219195597" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (HSS->NSS).", "chr_id": "12", "chr_pos": "78175326", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1668", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.1655.1655", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8IVL0-1.1663.1663", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.1672.1672", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8IVL0-1.1676.1676", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.1678.1678", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8IVL0-1.1679.1679", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8IVL0-1.1682.1682", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.1685.1685", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1672.1672", "start_pos": 1672, "end_pos": 1672, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2139648247", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139648247", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2139648247", "url": "https://www.ensembl.org/id/rs2139648247", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LNGPDHPPKDLRIRRQHSSE", "down_seq": "VSSINSATSHSSIGSGNDAD", "snv": [ { "evidence": [ { "id": "rs2139648247", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139648247" }, { "id": "rs2139648247", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2139648247" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SVS->NVS).", "chr_id": "12", "chr_pos": "78175339", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1672", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.1655.1655", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.1663.1663", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.1668.1668", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.1676.1676", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.1678.1678", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8IVL0-1.1679.1679", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.1682.1682", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.1685.1685", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.1691.1691", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1676.1676", "start_pos": 1676, "end_pos": 1676, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs61754963", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61754963", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs61754963", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61754963", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs61754963", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61754963", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs61754963", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61754963#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs61754963", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61754963", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "DHPPKDLRIRRQHSSESVSS", "down_seq": "NSATSHSSIGSGNDADSKKK", "snv": [ { "evidence": [ { "id": "rs61754963", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61754963" }, { "id": "rs61754963", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61754963" }, { "id": "rs61754963", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61754963" }, { "id": "rs61754963", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61754963#frequency_tab" }, { "id": "rs61754963", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61754963" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (INS->NNS).", "chr_id": "12", "chr_pos": "78175351", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1676", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.1663.1663", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8IVL0-1.1668.1668", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.1672.1672", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.1678.1678", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8IVL0-1.1679.1679", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.1682.1682", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.1685.1685", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.1691.1691", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1678.1678", "start_pos": 1678, "end_pos": 1678, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs755066674", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755066674", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs755066674", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755066674", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs755066674", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755066674#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs755066674", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755066674", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PPKDLRIRRQHSSESVSSIN", "down_seq": "ATSHSSIGSGNDADSKKKKK", "snv": [ { "evidence": [ { "id": "rs755066674", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755066674" }, { "id": "rs755066674", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755066674" }, { "id": "rs755066674", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs755066674#frequency_tab" }, { "id": "rs755066674", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755066674" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SAT->NAT).", "chr_id": "12", "chr_pos": "78175357", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1678", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.1663.1663", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.1668.1668", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.1672.1672", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.1676.1676", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.1679.1679", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.1682.1682", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8IVL0-1.1685.1685", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.1691.1691", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1679.1679", "start_pos": 1679, "end_pos": 1679, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PKDLRIRRQHSSESVSSINS", "down_seq": "TSHSSIGSGNDADSKKKKKK", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NSA->NST).", "chr_id": "12", "chr_pos": "78175359", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A1679", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8IVL0-1.1663.1663", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8IVL0-1.1668.1668", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8IVL0-1.1672.1672", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8IVL0-1.1676.1676", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.1678.1678", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8IVL0-1.1682.1682", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.1685.1685", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8IVL0-1.1691.1691", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1682.1682", "start_pos": 1682, "end_pos": 1682, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2139649456", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139649456", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2139649456", "url": "https://www.ensembl.org/id/rs2139649456", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "LRIRRQHSSESVSSINSATS", "down_seq": "SSIGSGNDADSKKKKKKNWV", "snv": [ { "evidence": [ { "id": "rs2139649456", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139649456" }, { "id": "rs2139649456", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2139649456" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HSS->NSS).", "chr_id": "12", "chr_pos": "78175368", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1682", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.1663.1663", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8IVL0-1.1668.1668", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.1672.1672", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.1676.1676", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.1678.1678", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8IVL0-1.1679.1679", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8IVL0-1.1685.1685", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.1691.1691", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1685.1685", "start_pos": 1685, "end_pos": 1685, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs932100888", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs932100888", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs932100888", "url": "https://www.ncbi.nlm.nih.gov/snp/rs932100888#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs932100888", "url": "http://gnomad.broadinstitute.org/awesome?query=rs932100888", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "RRQHSSESVSSINSATSHSS", "down_seq": "GSGNDADSKKKKKKNWVNSR", "snv": [ { "evidence": [ { "id": "rs932100888", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs932100888" }, { "id": "rs932100888", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs932100888#frequency_tab" }, { "id": "rs932100888", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs932100888" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IGS->NGS).", "chr_id": "12", "chr_pos": "78175378", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1685", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.1668.1668", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.1672.1672", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.1676.1676", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8IVL0-1.1678.1678", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.1679.1679", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8IVL0-1.1682.1682", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.1691.1691", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1691.1691", "start_pos": 1691, "end_pos": 1691, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2139650658", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139650658", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2139650658", "url": "https://www.ensembl.org/id/rs2139650658", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "ESVSSINSATSHSSIGSGND", "down_seq": "DSKKKKKKNWVNSRGSELRS", "snv": [ { "evidence": [ { "id": "rs2139650658", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139650658" }, { "id": "rs2139650658", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2139650658" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDA->NDS).", "chr_id": "12", "chr_pos": "78175395", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1691", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2139650658", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139650658" }, { "id": "rs2139650658", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2139650658" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDA->NDT).", "chr_id": "12", "chr_pos": "78175395", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1691", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.1672.1672", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.1676.1676", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.1678.1678", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8IVL0-1.1679.1679", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.1682.1682", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.1685.1685", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1737.1737", "start_pos": 1737, "end_pos": 1737, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1958270052", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1958270052", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1958270052", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1958270052#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "FGKKKSTKPPSSHSDIEELT", "down_seq": "SSLPASPKLPHNAGDCGSAS", "snv": [ { "evidence": [ { "id": "rs1958270052", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1958270052" }, { "id": "rs1958270052", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1958270052#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DSS->NSS).", "chr_id": "12", "chr_pos": "78177225", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1737", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.1741.1741", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8IVL0-1.1751.1751", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1741.1741", "start_pos": 1741, "end_pos": 1741, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "KSTKPPSSHSDIEELTDSSL", "down_seq": "ASPKLPHNAGDCGSASMKPS", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78177238", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P1741", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.1737.1737", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.1751.1751", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1751.1751", "start_pos": 1751, "end_pos": 1751, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1958273577", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1958273577", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1958273577", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1958273577#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "DIEELTDSSLPASPKLPHNA", "down_seq": "DCGSASMKPSQSASASPLVW", "snv": [ { "evidence": [ { "id": "rs1958273577", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1958273577" }, { "id": "rs1958273577", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1958273577#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NAG->NAS).", "chr_id": "12", "chr_pos": "78177267", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G1751", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q8IVL0-1.1737.1737", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.1741.1741", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.178.178", "start_pos": 178, "end_pos": 178, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757718301", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757718301", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757718301", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs757718301", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs757718301", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757718301", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757718301", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757718301", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GLSAEEIRNGNLKAILGLFF", "down_seq": "LSRYKQQQHHQQQYYQSLVE", "snv": [ { "evidence": [ { "id": "rs757718301", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757718301" }, { "id": "rs757718301", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs757718301" }, { "id": "rs757718301", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757718301" }, { "id": "rs757718301", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757718301" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SLS->NLS).", "chr_id": "12", "chr_pos": "77968564", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S178", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.193.193", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1815.1815", "start_pos": 1815, "end_pos": 1815, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AEAEIILQLKSELREKELKL", "down_seq": "DIRLEALSSAHHLDQIREAM", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78179609", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T1815", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1860.1860", "start_pos": 1860, "end_pos": 1860, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2139733854", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139733854", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2139733854", "url": "https://www.ensembl.org/id/rs2139733854", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "NEIEILKAENDRLKAETGNT", "down_seq": "KPTRPPSESSSSTSSSSSRQ", "snv": [ { "evidence": [ { "id": "rs2139733854", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139733854" }, { "id": "rs2139733854", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2139733854" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTA->NTT).", "chr_id": "12", "chr_pos": "78180931", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A1860", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q8IVL0-1.1871.1871", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8IVL0-1.1872.1872", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.1873.1873", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1871.1871", "start_pos": 1871, "end_pos": 1871, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2139735508", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139735508", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2139735508", "url": "https://www.ensembl.org/id/rs2139735508", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RLKAETGNTAKPTRPPSESS", "down_seq": "STSSSSSRQSLGLSLNNLNI", "snv": [ { "evidence": [ { "id": "rs2139735508", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139735508" }, { "id": "rs2139735508", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2139735508" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SST->NST).", "chr_id": "12", "chr_pos": "78180965", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1871", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8IVL0-1.1860.1860", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.1872.1872", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.1873.1873", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1872.1872", "start_pos": 1872, "end_pos": 1872, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1958472813", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1958472813", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1958472813", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1958472813#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LKAETGNTAKPTRPPSESSS", "down_seq": "TSSSSSRQSLGLSLNNLNIT", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs1958472813", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1958472813" }, { "id": "rs1958472813", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1958472813#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (STS->NTS).", "chr_id": "12", "chr_pos": "78180968", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1872", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8IVL0-1.1860.1860", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.1871.1871", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.1873.1873", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1873.1873", "start_pos": 1873, "end_pos": 1873, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2139735812", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139735812", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2139735812", "url": "https://www.ensembl.org/id/rs2139735812", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2139735812", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2139735812", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KAETGNTAKPTRPPSESSSS", "down_seq": "SSSSSRQSLGLSLNNLNITE", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs2139735812", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139735812" }, { "id": "rs2139735812", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2139735812" }, { "id": "rs2139735812", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2139735812" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TSS->NSS).", "chr_id": "12", "chr_pos": "78180971", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T1873", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.1860.1860", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.1871.1871", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.1872.1872", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1906.1906", "start_pos": 1906, "end_pos": 1906, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs763489074", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763489074", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763489074", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763489074", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763489074", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763489074", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LNNLNITEAVSSDILLDDAG", "down_seq": "ATGHKDGRSVKIIVSISKGY", "snv": [ { "evidence": [ { "id": "rs763489074", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763489074" }, { "id": "rs763489074", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763489074" }, { "id": "rs763489074", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763489074" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DAT->NAT).", "chr_id": "12", "chr_pos": "78185624", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1906", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.193.193", "start_pos": 193, "end_pos": 193, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2137991339", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137991339", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2137991339", "url": "https://www.ensembl.org/id/rs2137991339", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LGLFFSLSRYKQQQHHQQQY", "down_seq": "QSLVELQQRVTHASPPSEAS", "snv": [ { "evidence": [ { "id": "rs2137991339", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137991339" }, { "id": "rs2137991339", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2137991339" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YQS->NQS).", "chr_id": "12", "chr_pos": "77968608", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y193", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.210.210", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1969.1969", "start_pos": 1969, "end_pos": 1969, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2139850421", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139850421", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2139850421", "url": "https://www.ensembl.org/id/rs2139850421", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KWDVLDGVIRRLFKEYVFRI", "down_seq": "TSTSLGLSSDCIASYCIGDL", "snv": [ { "evidence": [ { "id": "rs2139850421", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139850421" }, { "id": "rs2139850421", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2139850421" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DTS->NTS).", "chr_id": "12", "chr_pos": "78188627", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1969", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q8IVL0-1.1981.1981", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8IVL0-1.1983.1983", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1981.1981", "start_pos": 1981, "end_pos": 1981, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2139852243", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139852243", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2139852243", "url": "https://www.ensembl.org/id/rs2139852243", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "FKEYVFRIDTSTSLGLSSDC", "down_seq": "ASYCIGDLIRSHNLEVPELL", "snv": [ { "evidence": [ { "id": "rs2139852243", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139852243" }, { "id": "rs2139852243", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2139852243" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IAS->NAS).", "chr_id": "12", "chr_pos": "78188664", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1981", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8IVL0-1.1969.1969", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.1983.1983", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.1990.1990", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1983.1983", "start_pos": 1983, "end_pos": 1983, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2139852510", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139852510", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2139852510", "url": "https://www.ensembl.org/id/rs2139852510", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EYVFRIDTSTSLGLSSDCIA", "down_seq": "YCIGDLIRSHNLEVPELLPC", "snv": [ { "evidence": [ { "id": "rs2139852510", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139852510" }, { "id": "rs2139852510", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2139852510" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SYC->NYC).", "chr_id": "12", "chr_pos": "78188670", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1983", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q8IVL0-1.1969.1969", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.1981.1981", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8IVL0-1.1990.1990", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1990.1990", "start_pos": 1990, "end_pos": 1990, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2139853412", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139853412", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2139853412", "url": "https://www.ensembl.org/id/rs2139853412", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "TSTSLGLSSDCIASYCIGDL", "down_seq": "RSHNLEVPELLPCGYLVGDN", "snv": [ { "evidence": [ { "id": "rs2139853412", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2139853412" }, { "id": "rs2139853412", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2139853412" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IRS->NRS).", "chr_id": "12", "chr_pos": "78188691", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1990", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.1981.1981", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8IVL0-1.1983.1983", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2012.2012", "start_pos": 2012, "end_pos": 2012, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1435691613", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1435691613", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1435691613", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1435691613#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1435691613", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1435691613", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1435691613", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1435691613", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "SHNLEVPELLPCGYLVGDNN", "down_seq": "ITVNLKGVEENSLDSFVFDT", "snv": [ { "evidence": [ { "id": "rs1435691613", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1435691613" }, { "id": "rs1435691613", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1435691613#frequency_tab" }, { "id": "rs1435691613", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1435691613" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IIT->NIT).", "chr_id": "12", "chr_pos": "78188757", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I2012", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "I", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NNI->NNS).", "chr_id": "12", "chr_pos": "78190029", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "I2012", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs1435691613", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1435691613" }, { "id": "rs1435691613", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1435691613#frequency_tab" }, { "id": "rs1435691613", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1435691613" }, { "id": "rs1435691613", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1435691613" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "I", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NNI->NNT).", "chr_id": "12", "chr_pos": "78188757", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "I2012", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.2013.2013", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.2025.2025", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2013.2013", "start_pos": 2013, "end_pos": 2013, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1958839527", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1958839527", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1958839527", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1958839527", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "HNLEVPELLPCGYLVGDNNI", "down_seq": "TVNLKGVEENSLDSFVFDTL", "snv": [ { "evidence": [ { "id": "rs1958839527", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1958839527" }, { "id": "rs1958839527", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1958839527" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NII->NIS).", "chr_id": "12", "chr_pos": "78188760", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I2013", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.2012.2012", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8IVL0-1.2025.2025", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2025.2025", "start_pos": 2025, "end_pos": 2025, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1395408755", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1395408755", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1395408755", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1395408755", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1395408755", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1395408755", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "YLVGDNNIITVNLKGVEENS", "down_seq": "DSFVFDTLIPKPITQRYFNL", "snv": [ { "evidence": [ { "id": "rs1395408755", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1395408755" }, { "id": "rs1395408755", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1395408755" }, { "id": "rs1395408755", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1395408755" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NSL->NSS).", "chr_id": "12", "chr_pos": "78190002", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L2025", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.2012.2012", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8IVL0-1.2013.2013", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.2040.2040", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.202.202", "start_pos": 202, "end_pos": 202, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "YKQQQHHQQQYYQSLVELQQ", "down_seq": "VTHASPPSEASQAKTQQDMQ", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "77968635", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R202", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8IVL0-1.210.210", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2040.2040", "start_pos": 2040, "end_pos": 2040, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "VEENSLDSFVFDTLIPKPIT", "down_seq": "RYFNLLMEHHRIILSGPSGT", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "Q", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "12", "chr_pos": "78190046", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q2040", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.2025.2025", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8IVL0-1.2058.2058", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2058.2058", "start_pos": 2058, "end_pos": 2058, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs183717093", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs183717093", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs183717093", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs183717093", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs183717093", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs183717093", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs183717093", "url": "https://www.ncbi.nlm.nih.gov/snp/rs183717093#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs183717093", "url": "http://gnomad.broadinstitute.org/awesome?query=rs183717093", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ITQRYFNLLMEHHRIILSGP", "down_seq": "GTGKTYLANKLAEYVITKSG", "snv": [ { "evidence": [ { "id": "rs183717093", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs183717093" }, { "id": "rs183717093", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs183717093" }, { "id": "rs183717093", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs183717093" }, { "id": "rs183717093", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs183717093#frequency_tab" }, { "id": "rs183717093", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs183717093" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SGT->NGT).", "chr_id": "12", "chr_pos": "78190101", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "S2058", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8IVL0-1.2040.2040", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.2075.2075", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2075.2075", "start_pos": 2075, "end_pos": 2075, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs137872640", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs137872640", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs137872640", "url": "http://gnomad.broadinstitute.org/awesome?query=rs137872640", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SGPSGTGKTYLANKLAEYVI", "down_seq": "KSGRKKTEDAIATFNVDHKS", "snv": [ { "evidence": [ { "id": "rs137872640", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs137872640" }, { "id": "rs137872640", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs137872640" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TKS->NKS).", "chr_id": "12", "chr_pos": "78190152", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T2075", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.2058.2058", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8IVL0-1.2093.2093", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2093.2093", "start_pos": 2093, "end_pos": 2093, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1171848406", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1171848406", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1171848406", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1171848406#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1171848406", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1171848406", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "VITKSGRKKTEDAIATFNVD", "down_seq": "KSSKELQQYLANLAEQCSAD", "snv": [ { "evidence": [ { "id": "rs1171848406", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1171848406" }, { "id": "rs1171848406", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1171848406#frequency_tab" }, { "id": "rs1171848406", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1171848406" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HKS->NKS).", "chr_id": "12", "chr_pos": "78190205", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H2093", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8IVL0-1.2075.2075", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8IVL0-1.2107.2107", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2107.2107", "start_pos": 2107, "end_pos": 2107, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "ATFNVDHKSSKELQQYLANL", "down_seq": "EQCSADNNGVELPVVIILDN", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NLA->NLS).", "chr_id": "12", "chr_pos": "78197274", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A2107", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q8IVL0-1.2093.2093", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.210.210", "start_pos": 210, "end_pos": 210, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QQYYQSLVELQQRVTHASPP", "down_seq": "EASQAKTQQDMQSSLAARYA", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "77968660", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S210", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8IVL0-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.229.229", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2141.2141", "start_pos": 2141, "end_pos": 2141, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1436486803", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1436486803", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1436486803", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1436486803", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "VVIILDNLHHVGSLSDIFNG", "down_seq": "LNCKYNKCPYIIGTMNQGVS", "snv": [ { "evidence": [ { "id": "rs1436486803", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1436486803" }, { "id": "rs1436486803", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1436486803" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGF->NGC).", "chr_id": "12", "chr_pos": "78197377", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F2141", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.2145.2145", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2145.2145", "start_pos": 2145, "end_pos": 2145, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1229917843", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1229917843", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1229917843", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1229917843", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LDNLHHVGSLSDIFNGFLNC", "down_seq": "YNKCPYIIGTMNQGVSSSPN", "snv": [ { "evidence": [ { "id": "rs1229917843", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1229917843" }, { "id": "rs1229917843", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1229917843" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NCK->NCT).", "chr_id": "12", "chr_pos": "78197389", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K2145", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.2141.2141", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2173.2173", "start_pos": 2173, "end_pos": 2173, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2140009632", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2140009632", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2140009632", "url": "https://www.ensembl.org/id/rs2140009632", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IGTMNQGVSSSPNLELHHNF", "down_seq": "WVLCANHTEPVKGFLGRYLR", "snv": [ { "evidence": [ { "id": "rs2140009632", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2140009632" }, { "id": "rs2140009632", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2140009632" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NFR->NFS).", "chr_id": "12", "chr_pos": "78199335", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R2173", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "Q8IVL0-1.2193.2193", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2193.2193", "start_pos": 2193, "end_pos": 2193, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RWVLCANHTEPVKGFLGRYL", "down_seq": "RKLIEIEIERNIRNNDLVKI", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78199393", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R2193", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8IVL0-1.2173.2173", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.2206.2206", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2206.2206", "start_pos": 2206, "end_pos": 2206, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs371772901", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371772901", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371772901", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371772901", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs371772901", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371772901#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs371772901", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371772901", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs371772901", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs371772901", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GFLGRYLRRKLIEIEIERNI", "down_seq": "NNDLVKIIDWIPKTWHHLNS", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs371772901", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371772901" }, { "id": "rs371772901", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371772901" }, { "id": "rs371772901", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371772901#frequency_tab" }, { "id": "rs371772901", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371772901" }, { "id": "rs371772901", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs371772901" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NIR->NIC).", "chr_id": "12", "chr_pos": "78199432", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R2206", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs371772901", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371772901" }, { "id": "rs371772901", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371772901" }, { "id": "rs371772901", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371772901#frequency_tab" }, { "id": "rs371772901", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371772901" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIR->NIS).", "chr_id": "12", "chr_pos": "78199432", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R2206", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.2193.2193", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2232.2232", "start_pos": 2232, "end_pos": 2232, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2140015805", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2140015805", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2140015805", "url": "https://www.ensembl.org/id/rs2140015805", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KIIDWIPKTWHHLNSFLETH", "down_seq": "SSDVTIGPRLFLPCPMDVEG", "snv": [ { "evidence": [ { "id": "rs2140015805", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2140015805" }, { "id": "rs2140015805", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2140015805" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SSS->NSS).", "chr_id": "12", "chr_pos": "78199511", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2232", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q8IVL0-1.2235.2235", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2235.2235", "start_pos": 2235, "end_pos": 2235, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2140016017", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2140016017", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2140016017", "url": "https://www.ensembl.org/id/rs2140016017", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2140016017", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2140016017", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "DWIPKTWHHLNSFLETHSSS", "down_seq": "VTIGPRLFLPCPMDVEGSRV", "snv": [ { "evidence": [ { "id": "rs2140016017", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2140016017" }, { "id": "rs2140016017", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2140016017" }, { "id": "rs2140016017", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2140016017" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DVT->NVT).", "chr_id": "12", "chr_pos": "78199519", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D2235", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q8IVL0-1.2232.2232", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.229.229", "start_pos": 229, "end_pos": 229, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2136401333", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136401333", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136401333", "url": "https://www.ensembl.org/id/rs2136401333", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "PSEASQAKTQQDMQSSLAAR", "down_seq": "ATQSNHSGIATSQKKPTRLP", "snv": [ { "evidence": [ { "id": "rs2136401333", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136401333" }, { "id": "rs2136401333", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136401333" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YAT->NAT).", "chr_id": "12", "chr_pos": "77994816", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y229", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.239.239", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2315.2315", "start_pos": 2315, "end_pos": 2315, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DTYPWSSATLPQESPALLQL", "down_seq": "PEDVGYESCTSTKEATTSKH", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78205044", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R2315", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2367.2367", "start_pos": 2367, "end_pos": 2367, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2140139810", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2140139810", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2140139810", "url": "https://www.ensembl.org/id/rs2140139810", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MNMLMKLQEAANYSSTQSCD", "down_seq": "ESTSHHEDILDSSLESTL", "snv": [ { "evidence": [ { "id": "rs2140139810", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2140139810" }, { "id": "rs2140139810", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2140139810" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SES->NES).", "chr_id": "12", "chr_pos": "78210459", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2367", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.2369.2369", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8IVL0-1.2378.2378", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2369.2369", "start_pos": 2369, "end_pos": 2369, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs764074467", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764074467", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764074467", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764074467", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764074467", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764074467#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs764074467", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764074467", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MLMKLQEAANYSSTQSCDSE", "down_seq": "TSHHEDILDSSLESTL", "snv": [ { "evidence": [ { "id": "rs764074467", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764074467" }, { "id": "rs764074467", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764074467" }, { "id": "rs764074467", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764074467#frequency_tab" }, { "id": "rs764074467", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764074467" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (STS->NTS).", "chr_id": "12", "chr_pos": "78210465", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S2369", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.2367.2367", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.2378.2378", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.2378.2378", "start_pos": 2378, "end_pos": 2378, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "NYSSTQSCDSESTSHHEDIL", "down_seq": "SSLESTL", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DSS->NSS).", "chr_id": "12", "chr_pos": "78210491", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D2378", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8IVL0-1.2367.2367", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.2369.2369", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.238.238", "start_pos": 238, "end_pos": 238, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2136402231", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136402231", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136402231", "url": "https://www.ensembl.org/id/rs2136402231", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "QQDMQSSLAARYATQSNHSG", "down_seq": "ATSQKKPTRLPGPSRVPAAG", "snv": [ { "evidence": [ { "id": "rs2136402231", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136402231" }, { "id": "rs2136402231", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136402231" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IAT->NAT).", "chr_id": "12", "chr_pos": "77994844", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I238", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.239.239", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.239.239", "start_pos": 239, "end_pos": 239, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QDMQSSLAARYATQSNHSGI", "down_seq": "TSQKKPTRLPGPSRVPAAGS", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "77994846", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A239", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.229.229", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.238.238", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.270.270", "start_pos": 270, "end_pos": 270, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs781245455", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781245455", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781245455", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781245455", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781245455", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781245455", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GPSRVPAAGSSSKVQGASNL", "down_seq": "RRSQSFNSIDKNKPPNYANG", "snv": [ { "evidence": [ { "id": "rs781245455", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781245455" }, { "id": "rs781245455", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781245455" }, { "id": "rs781245455", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781245455" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLN->NLS).", "chr_id": "12", "chr_pos": "77998405", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N270", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q8IVL0-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8IVL0-1.288.288", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.284.284", "start_pos": 284, "end_pos": 284, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs780001706", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780001706", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780001706", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780001706", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780001706", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780001706", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "QGASNLNRRSQSFNSIDKNK", "down_seq": "PNYANGNEKDSSKGPQSSSG", "snv": [ { "evidence": [ { "id": "rs780001706", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780001706" }, { "id": "rs780001706", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780001706" }, { "id": "rs780001706", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780001706" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKP->NKS).", "chr_id": "12", "chr_pos": "78050981", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P284", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs780001706", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780001706" }, { "id": "rs780001706", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780001706" }, { "id": "rs780001706", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780001706" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NKP->NKT).", "chr_id": "12", "chr_pos": "77998446", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P284", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q8IVL0-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.294.294", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.288.288", "start_pos": 288, "end_pos": 288, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2137256703", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137256703", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2137256703", "url": "https://www.ensembl.org/id/rs2137256703", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs772446522", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772446522", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772446522", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772446522", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772446522", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772446522#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs772446522", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772446522", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "NLNRRSQSFNSIDKNKPPNY", "down_seq": "NGNEKDSSKGPQSSSGVNGN", "snv": [ { "evidence": [ { "id": "rs2137256703", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137256703" }, { "id": "rs2137256703", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2137256703" }, { "id": "rs772446522", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772446522" }, { "id": "rs772446522", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772446522" }, { "id": "rs772446522", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772446522#frequency_tab" }, { "id": "rs772446522", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772446522" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NYA->NYT).", "chr_id": "12", "chr_pos": "78050993", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A288", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8IVL0-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8IVL0-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8IVL0-1.308.308", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.293.293", "start_pos": 293, "end_pos": 293, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs747060237", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747060237", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747060237", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747060237", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747060237", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747060237#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs747060237", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747060237", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SQSFNSIDKNKPPNYANGNE", "down_seq": "DSSKGPQSSSGVNGNVQPPS", "snv": [ { "evidence": [ { "id": "rs747060237", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747060237" }, { "id": "rs747060237", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747060237" }, { "id": "rs747060237", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747060237#frequency_tab" }, { "id": "rs747060237", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747060237" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KDS->NDS).", "chr_id": "12", "chr_pos": "77998475", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K293", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8IVL0-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.308.308", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.294.294", "start_pos": 294, "end_pos": 294, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1294312017", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1294312017", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1294312017", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1294312017", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QSFNSIDKNKPPNYANGNEK", "down_seq": "SSKGPQSSSGVNGNVQPPST", "snv": [ { "evidence": [ { "id": "rs1294312017", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1294312017" }, { "id": "rs1294312017", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1294312017" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DSS->NSS).", "chr_id": "12", "chr_pos": "77998476", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D294", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8IVL0-1.308.308", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.308.308", "start_pos": 308, "end_pos": 308, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs758010168", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758010168", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758010168", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758010168", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758010168", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758010168", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs758010168", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs758010168", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ANGNEKDSSKGPQSSSGVNG", "down_seq": "VQPPSTAGQPPASAIPSPSA", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs758010168", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758010168" }, { "id": "rs758010168", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758010168" }, { "id": "rs758010168", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758010168" }, { "id": "rs758010168", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs758010168" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NGN->NGT).", "chr_id": "12", "chr_pos": "78006461", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N308", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8IVL0-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8IVL0-1.294.294", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.32.32", "start_pos": 32, "end_pos": 32, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1446195086", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1446195086", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1446195086", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1446195086", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1446195086", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1446195086", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QPAVGSKPVHTALPIPNLGT", "down_seq": "GSQHCSSRPLELTETESSML", "snv": [ { "evidence": [ { "id": "rs1446195086", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1446195086" }, { "id": "rs1446195086", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1446195086" }, { "id": "rs1446195086", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1446195086" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TGS->NGS).", "chr_id": "12", "chr_pos": "77831556", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T32", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.45.45", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.334.334", "start_pos": 334, "end_pos": 334, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2136559029", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136559029", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136559029", "url": "https://www.ensembl.org/id/rs2136559029", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TAGQPPASAIPSPSASKPWR", "down_seq": "KSMNVKHSATSTMLTVKQSS", "snv": [ { "evidence": [ { "id": "rs2136559029", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136559029" }, { "id": "rs2136559029", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136559029" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SKS->NKS).", "chr_id": "12", "chr_pos": "78006539", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S334", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8IVL0-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.351.351", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.340.340", "start_pos": 340, "end_pos": 340, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs373918851", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373918851", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs373918851", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373918851", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs373918851", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373918851", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ASAIPSPSASKPWRSKSMNV", "down_seq": "HSATSTMLTVKQSSTATSPT", "snv": [ { "evidence": [ { "id": "rs373918851", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373918851" }, { "id": "rs373918851", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373918851" }, { "id": "rs373918851", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373918851" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KHS->NHS).", "chr_id": "12", "chr_pos": "78006558", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K340", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q8IVL0-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8IVL0-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8IVL0-1.360.360", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.342.342", "start_pos": 342, "end_pos": 342, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1874255667", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1874255667", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1874255667", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1874255667#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AIPSPSASKPWRSKSMNVKH", "down_seq": "ATSTMLTVKQSSTATSPTPS", "snv": [ { "evidence": [ { "id": "rs1874255667", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1874255667" }, { "id": "rs1874255667", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1874255667#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SAT->NAT).", "chr_id": "12", "chr_pos": "78006563", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S342", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8IVL0-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8IVL0-1.360.360", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.344.344", "start_pos": 344, "end_pos": 344, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2136560232", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136560232", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136560232", "url": "https://www.ensembl.org/id/rs2136560232", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2136560232", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2136560232", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PSPSASKPWRSKSMNVKHSA", "down_seq": "STMLTVKQSSTATSPTPSSD", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs2136560232", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136560232" }, { "id": "rs2136560232", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136560232" }, { "id": "rs2136560232", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2136560232" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TST->NST).", "chr_id": "12", "chr_pos": "78006569", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T344", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8IVL0-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8IVL0-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8IVL0-1.360.360", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.351.351", "start_pos": 351, "end_pos": 351, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs983673259", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs983673259", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs983673259", "url": "https://www.ensembl.org/id/rs983673259", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PWRSKSMNVKHSATSTMLTV", "down_seq": "QSSTATSPTPSSDRLKPPVS", "snv": [ { "evidence": [ { "id": "rs983673259", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs983673259" }, { "id": "rs983673259", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs983673259" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KQS->NQS).", "chr_id": "12", "chr_pos": "78006591", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K351", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8IVL0-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8IVL0-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8IVL0-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.360.360", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.36.36", "start_pos": 36, "end_pos": 36, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2136076879", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136076879", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136076879", "url": "https://www.ensembl.org/id/rs2136076879", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "GSKPVHTALPIPNLGTTGSQ", "down_seq": "CSSRPLELTETESSMLSCQL", "snv": [ { "evidence": [ { "id": "rs2136076879", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136076879" }, { "id": "rs2136076879", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136076879" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HCS->NCS).", "chr_id": "12", "chr_pos": "77831567", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H36", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.45.45", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.398.398", "start_pos": 398, "end_pos": 398, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PSGQKSMLEKFKLVNARTAL", "down_seq": "PPQPPSSGPSDGGKDDDAFS", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78006730", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R398", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q8IVL0-1.406.406", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.406.406", "start_pos": 406, "end_pos": 406, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "EKFKLVNARTALRPPQPPSS", "down_seq": "PSDGGKDDDAFSESGEMEGF", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78006754", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G406", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8IVL0-1.398.398", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.429.429", "start_pos": 429, "end_pos": 429, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200010458", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200010458", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200010458", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200010458", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs200010458", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200010458", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200010458", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200010458#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200010458", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200010458", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "DGGKDDDAFSESGEMEGFNS", "down_seq": "LNSGGSTNSSPKVSPKLAPP", "snv": [ { "evidence": [ { "id": "rs200010458", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200010458" }, { "id": "rs200010458", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200010458" }, { "id": "rs200010458", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200010458" }, { "id": "rs200010458", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200010458#frequency_tab" }, { "id": "rs200010458", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200010458" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSG->NSC).", "chr_id": "12", "chr_pos": "78006823", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.00117739", "site_lbl": "G429", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs200010458", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200010458" }, { "id": "rs200010458", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200010458" }, { "id": "rs200010458", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200010458" }, { "id": "rs200010458", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200010458#frequency_tab" }, { "id": "rs200010458", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200010458" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSG->NSS).", "chr_id": "12", "chr_pos": "78006823", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.00117739", "site_lbl": "G429", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.433.433", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8IVL0-1.437.437", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.439.439", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8IVL0-1.440.440", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8IVL0-1.441.441", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.433.433", "start_pos": 433, "end_pos": 433, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200389736", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200389736", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200389736", "url": "https://www.ensembl.org/id/rs200389736", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "DDDAFSESGEMEGFNSGLNS", "down_seq": "GSTNSSPKVSPKLAPPKAGS", "snv": [ { "evidence": [ { "id": "rs200389736", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200389736" }, { "id": "rs200389736", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs200389736" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSG->NSC).", "chr_id": "12", "chr_pos": "78006835", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G433", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.429.429", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.437.437", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.439.439", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8IVL0-1.440.440", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8IVL0-1.441.441", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.439.439", "start_pos": 439, "end_pos": 439, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2136573944", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136573944", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136573944", "url": "https://www.ensembl.org/id/rs2136573944", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1402842188", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1402842188", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1402842188", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1402842188", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ESGEMEGFNSGLNSGGSTNS", "down_seq": "PKVSPKLAPPKAGSKNLSNK", "snv": [ { "evidence": [ { "id": "rs2136573944", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136573944" }, { "id": "rs2136573944", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136573944" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->NSG).", "chr_id": "12", "chr_pos": "78006853", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S439", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1402842188", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1402842188" }, { "id": "rs1402842188", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1402842188" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->NSI).", "chr_id": "12", "chr_pos": "78006854", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S439", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1402842188", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1402842188" }, { "id": "rs1402842188", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1402842188" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->NSN).", "chr_id": "12", "chr_pos": "78006854", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S439", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.429.429", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.433.433", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.437.437", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.440.440", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.441.441", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8IVL0-1.459.459", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.440.440", "start_pos": 440, "end_pos": 440, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "SGEMEGFNSGLNSGGSTNSS", "down_seq": "KVSPKLAPPKAGSKNLSNKK", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78006856", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P440", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8IVL0-1.429.429", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8IVL0-1.433.433", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8IVL0-1.437.437", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.439.439", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.441.441", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.459.459", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.441.441", "start_pos": 441, "end_pos": 441, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2136574275", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136574275", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136574275", "url": "https://www.ensembl.org/id/rs2136574275", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2136574275", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2136574275", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "GEMEGFNSGLNSGGSTNSSP", "down_seq": "VSPKLAPPKAGSKNLSNKKS", "snv": [ { "evidence": [ { "id": "rs2136574275", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136574275" }, { "id": "rs2136574275", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136574275" }, { "id": "rs2136574275", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2136574275" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KVS->NVS).", "chr_id": "12", "chr_pos": "78006861", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K441", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8IVL0-1.429.429", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8IVL0-1.433.433", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.437.437", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.439.439", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.440.440", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8IVL0-1.459.459", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.459.459", "start_pos": 459, "end_pos": 459, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1275677024", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1275677024", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1275677024", "url": "https://www.ensembl.org/id/rs1275677024", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1275677024", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1275677024", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SPKVSPKLAPPKAGSKNLSN", "down_seq": "KSLLQPKEKEEKNRDKNKVC", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs1275677024", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1275677024" }, { "id": "rs1275677024", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1275677024" }, { "id": "rs1275677024", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1275677024" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KKS->NKS).", "chr_id": "12", "chr_pos": "78006915", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K459", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8IVL0-1.439.439", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.440.440", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8IVL0-1.441.441", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8IVL0-1.477.477", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PIPNLGTTGSQHCSSRPLEL", "down_seq": "ETESSMLSCQLALKSTCEFG", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "15", "frequency": "0.3", "sequence_org": "T", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: patient count (15/4799).", "chr_id": "12", "chr_pos": "77831594", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "T45", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8IVL0-1.59.59", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.477.477", "start_pos": 477, "end_pos": 477, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2136579533", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136579533", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136579533", "url": "https://www.ensembl.org/id/rs2136579533", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SNKKSLLQPKEKEEKNRDKN", "down_seq": "VCTEKPVKEEKDQVTEMAPK", "snv": [ { "evidence": [ { "id": "rs2136579533", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136579533" }, { "id": "rs2136579533", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136579533" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KVC->NVC).", "chr_id": "12", "chr_pos": "78006969", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K477", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8IVL0-1.459.459", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.498.498", "start_pos": 498, "end_pos": 498, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1874352790", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1874352790", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1874352790", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1874352790#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VCTEKPVKEEKDQVTEMAPK", "down_seq": "TSKIASLIPKGSKTTAAKKE", "snv": [ { "evidence": [ { "id": "rs1874352790", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1874352790" }, { "id": "rs1874352790", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1874352790#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KTS->NTS).", "chr_id": "12", "chr_pos": "78007032", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K498", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.502.502", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.508.508", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8IVL0-1.510.510", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.511.511", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.502.502", "start_pos": 502, "end_pos": 502, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2136583594", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136583594", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136583594", "url": "https://www.ensembl.org/id/rs2136583594", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "KPVKEEKDQVTEMAPKKTSK", "down_seq": "ASLIPKGSKTTAAKKESLIP", "snv": [ { "evidence": [ { "id": "rs2136583594", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136583594" }, { "id": "rs2136583594", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136583594" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IAS->NAS).", "chr_id": "12", "chr_pos": "78007043", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I502", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.498.498", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.508.508", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8IVL0-1.510.510", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.511.511", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.508.508", "start_pos": 508, "end_pos": 508, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs540019767", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs540019767", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs540019767", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs540019767", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs540019767", "url": "https://www.ncbi.nlm.nih.gov/snp/rs540019767#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs540019767", "url": "http://gnomad.broadinstitute.org/awesome?query=rs540019767", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs540019767", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs540019767", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KDQVTEMAPKKTSKIASLIP", "down_seq": "GSKTTAAKKESLIPSSSGIP", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs540019767", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs540019767" }, { "id": "rs540019767", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs540019767" }, { "id": "rs540019767", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs540019767#frequency_tab" }, { "id": "rs540019767", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs540019767" }, { "id": "rs540019767", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs540019767" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KGS->NGS).", "chr_id": "12", "chr_pos": "78007062", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "K508", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.498.498", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.502.502", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.510.510", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8IVL0-1.511.511", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.510.510", "start_pos": 510, "end_pos": 510, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs61754793", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61754793", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs61754793", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61754793", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs61754793", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61754793", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs61754793", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61754793#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs61754793", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61754793", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QVTEMAPKKTSKIASLIPKG", "down_seq": "KTTAAKKESLIPSSSGIPKP", "snv": [ { "evidence": [ { "id": "rs61754793", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61754793" }, { "id": "rs61754793", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61754793" }, { "id": "rs61754793", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61754793" }, { "id": "rs61754793", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61754793#frequency_tab" }, { "id": "rs61754793", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61754793" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SKT->NKT).", "chr_id": "12", "chr_pos": "78007067", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "S510", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8IVL0-1.498.498", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8IVL0-1.502.502", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.508.508", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.511.511", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.511.511", "start_pos": 511, "end_pos": 511, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs750238403", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750238403", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750238403", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750238403", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750238403", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750238403#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs750238403", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750238403", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs750238403", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs750238403", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs2138577127", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138577127", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138577127", "url": "https://www.ensembl.org/id/rs2138577127", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VTEMAPKKTSKIASLIPKGS", "down_seq": "TTAAKKESLIPSSSGIPKPG", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs750238403", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750238403" }, { "id": "rs750238403", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750238403" }, { "id": "rs750238403", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750238403#frequency_tab" }, { "id": "rs750238403", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750238403" }, { "id": "rs750238403", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs750238403" }, { "id": "rs2138577127", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138577127" }, { "id": "rs2138577127", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138577127" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KTT->NTT).", "chr_id": "12", "chr_pos": "78007071", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K511", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.498.498", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.502.502", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8IVL0-1.508.508", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.510.510", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.538.538", "start_pos": 538, "end_pos": 538, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2136588802", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136588802", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136588802", "url": "https://www.ensembl.org/id/rs2136588802", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ESLIPSSSGIPKPGSKVPTV", "down_seq": "QTISPGSTASKESEKFRTTK", "snv": [ { "evidence": [ { "id": "rs2136588802", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136588802" }, { "id": "rs2136588802", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136588802" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KQT->NQT).", "chr_id": "12", "chr_pos": "78007152", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K538", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.540.540", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8IVL0-1.549.549", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8IVL0-1.558.558", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.540.540", "start_pos": 540, "end_pos": 540, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2136589087", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136589087", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136589087", "url": "https://www.ensembl.org/id/rs2136589087", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LIPSSSGIPKPGSKVPTVKQ", "down_seq": "ISPGSTASKESEKFRTTKGS", "snv": [ { "evidence": [ { "id": "rs2136589087", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136589087" }, { "id": "rs2136589087", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136589087" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TIS->NIS).", "chr_id": "12", "chr_pos": "78007157", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T540", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.538.538", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.549.549", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8IVL0-1.558.558", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.549.549", "start_pos": 549, "end_pos": 549, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2136590628", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136590628", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136590628", "url": "https://www.ensembl.org/id/rs2136590628", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KPGSKVPTVKQTISPGSTAS", "down_seq": "ESEKFRTTKGSPSQSLSKPI", "snv": [ { "evidence": [ { "id": "rs2136590628", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136590628" }, { "id": "rs2136590628", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136590628" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KES->NES).", "chr_id": "12", "chr_pos": "78007185", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K549", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8IVL0-1.538.538", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.540.540", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.558.558", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.558.558", "start_pos": 558, "end_pos": 558, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs372042441", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372042441", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs372042441", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372042441", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs372042441", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372042441#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs372042441", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372042441", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KQTISPGSTASKESEKFRTT", "down_seq": "GSPSQSLSKPITMEKASASS", "snv": [ { "evidence": [ { "id": "rs372042441", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372042441" }, { "id": "rs372042441", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372042441" }, { "id": "rs372042441", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372042441#frequency_tab" }, { "id": "rs372042441", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372042441" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KGS->NGS).", "chr_id": "12", "chr_pos": "78007212", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K558", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8IVL0-1.538.538", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8IVL0-1.540.540", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.549.549", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.573.573", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.575.575", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.573.573", "start_pos": 573, "end_pos": 573, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2136594143", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136594143", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136594143", "url": "https://www.ensembl.org/id/rs2136594143", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KFRTTKGSPSQSLSKPITME", "down_seq": "ASASSCPAPLEGREAGQASP", "snv": [ { "evidence": [ { "id": "rs2136594143", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136594143" }, { "id": "rs2136594143", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136594143" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KAS->NAS).", "chr_id": "12", "chr_pos": "78007257", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K573", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.558.558", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.575.575", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.579.579", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.575.575", "start_pos": 575, "end_pos": 575, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2136594417", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136594417", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136594417", "url": "https://www.ensembl.org/id/rs2136594417", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RTTKGSPSQSLSKPITMEKA", "down_seq": "ASSCPAPLEGREAGQASPSG", "snv": [ { "evidence": [ { "id": "rs2136594417", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136594417" }, { "id": "rs2136594417", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136594417" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SAS->NAS).", "chr_id": "12", "chr_pos": "78007262", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S575", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.558.558", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.573.573", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.579.579", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.579.579", "start_pos": 579, "end_pos": 579, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "GSPSQSLSKPITMEKASASS", "down_seq": "PAPLEGREAGQASPSGSCTM", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "C", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78007274", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "C579", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.573.573", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.575.575", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.598.598", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.598.598", "start_pos": 598, "end_pos": 598, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2136597740", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136597740", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136597740", "url": "https://www.ensembl.org/id/rs2136597740", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SCPAPLEGREAGQASPSGSC", "down_seq": "MTVAQSSGQSTGNGAVQLPQ", "snv": [ { "evidence": [ { "id": "rs2136597740", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136597740" }, { "id": "rs2136597740", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136597740" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TMT->NMT).", "chr_id": "12", "chr_pos": "78007331", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T598", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.579.579", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.613.613", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.59.59", "start_pos": 59, "end_pos": 59, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2136078810", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136078810", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2136078810", "url": "https://www.ensembl.org/id/rs2136078810", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SRPLELTETESSMLSCQLAL", "down_seq": "STCEFGEKKPLQGKAKEKED", "snv": [ { "evidence": [ { "id": "rs2136078810", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2136078810" }, { "id": "rs2136078810", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2136078810" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KST->NST).", "chr_id": "12", "chr_pos": "77831638", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K59", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q8IVL0-1.45.45", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.613.613", "start_pos": 613, "end_pos": 613, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs780519676", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780519676", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780519676", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780519676", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780519676", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780519676", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PSGSCTMTVAQSSGQSTGNG", "down_seq": "VQLPQQQQHSHPNTATVAPF", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NGA->NGS).", "chr_id": "12", "chr_pos": "78007375", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A613", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs780519676", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780519676" }, { "id": "rs780519676", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780519676" }, { "id": "rs780519676", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780519676" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGA->NGT).", "chr_id": "12", "chr_pos": "78007375", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A613", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.598.598", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.628.628", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.628.628", "start_pos": 628, "end_pos": 628, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1348734842", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1348734842", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1348734842", "url": "https://www.ensembl.org/id/rs1348734842", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1348734842", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1348734842", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "STGNGAVQLPQQQQHSHPNT", "down_seq": "TVAPFIYRAHSENEGTALPS", "snv": [ { "evidence": [ { "id": "rs1348734842", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1348734842" }, { "id": "rs1348734842", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1348734842" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTA->NTS).", "chr_id": "12", "chr_pos": "78007420", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A628", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs1348734842", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1348734842" }, { "id": "rs1348734842", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1348734842" }, { "id": "rs1348734842", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1348734842" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NTA->NTT).", "chr_id": "12", "chr_pos": "78007420", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A628", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78007421", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A628", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.613.613", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.650.650", "start_pos": 650, "end_pos": 650, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757531299", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757531299", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757531299", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757531299", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757531299", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757531299", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VAPFIYRAHSENEGTALPSA", "down_seq": "SCTSPTKMDLSYSKTAKQCL", "snv": [ { "evidence": [ { "id": "rs757531299", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757531299" }, { "id": "rs757531299", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757531299" }, { "id": "rs757531299", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757531299" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DSC->NSC).", "chr_id": "12", "chr_pos": "78021787", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D650", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.659.659", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8IVL0-1.661.661", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.663.663", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.667.667", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.659.659", "start_pos": 659, "end_pos": 659, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1253562024", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1253562024", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1253562024", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1253562024#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1253562024", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1253562024", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SENEGTALPSADSCTSPTKM", "down_seq": "LSYSKTAKQCLEEISGEDPE", "snv": [ { "evidence": [ { "id": "rs1253562024", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1253562024" }, { "id": "rs1253562024", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1253562024#frequency_tab" }, { "id": "rs1253562024", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1253562024" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DLS->NLS).", "chr_id": "12", "chr_pos": "78021814", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D659", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.650.650", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.661.661", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.663.663", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8IVL0-1.667.667", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.661.661", "start_pos": 661, "end_pos": 661, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2138625790", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138625790", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138625790", "url": "https://www.ensembl.org/id/rs2138625790", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NEGTALPSADSCTSPTKMDL", "down_seq": "YSKTAKQCLEEISGEDPETR", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78021821", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S661", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs2138625790", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138625790" }, { "id": "rs2138625790", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138625790" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SYS->NYS).", "chr_id": "12", "chr_pos": "78119678", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S661", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8IVL0-1.650.650", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.659.659", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.663.663", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.667.667", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.663.663", "start_pos": 663, "end_pos": 663, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs754785923", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754785923", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs754785923", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754785923", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs754785923", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754785923", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GTALPSADSCTSPTKMDLSY", "down_seq": "KTAKQCLEEISGEDPETRRM", "snv": [ { "evidence": [ { "id": "rs754785923", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754785923" }, { "id": "rs754785923", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754785923" }, { "id": "rs754785923", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754785923" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SKT->NKT).", "chr_id": "12", "chr_pos": "78021827", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S663", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.650.650", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.659.659", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.661.661", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.667.667", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.667.667", "start_pos": 667, "end_pos": 667, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs769750648", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769750648", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769750648", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769750648", "database": "ExAC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PSADSCTSPTKMDLSYSKTA", "down_seq": "QCLEEISGEDPETRRMRTVK", "snv": [ { "evidence": [ { "id": "rs769750648", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769750648" }, { "id": "rs769750648", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769750648" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KQC->NQC).", "chr_id": "12", "chr_pos": "78021840", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K667", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.650.650", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8IVL0-1.659.659", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.661.661", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.663.663", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.690.690", "start_pos": 690, "end_pos": 690, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2137226573", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137226573", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2137226573", "url": "https://www.ensembl.org/id/rs2137226573", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LEEISGEDPETRRMRTVKNI", "down_seq": "DLRQNLEETMSSLRGTQISH", "snv": [ { "evidence": [ { "id": "rs2137226573", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137226573" }, { "id": "rs2137226573", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2137226573" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIA->NIS).", "chr_id": "12", "chr_pos": "78050037", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A690", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2137226573", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137226573" }, { "id": "rs2137226573", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2137226573" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIA->NIT).", "chr_id": "12", "chr_pos": "78050037", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A690", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q8IVL0-1.704.704", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.709.709", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8IVL0-1.710.710", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.704.704", "start_pos": 704, "end_pos": 704, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RTVKNIADLRQNLEETMSSL", "down_seq": "GTQISHSTLETTFDSTVTTE", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78050079", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R704", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q8IVL0-1.690.690", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8IVL0-1.709.709", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.710.710", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8IVL0-1.718.718", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.709.709", "start_pos": 709, "end_pos": 709, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs3905725", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3905725", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs3905725", "url": "https://www.ensembl.org/id/rs3905725", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IADLRQNLEETMSSLRGTQI", "down_seq": "HSTLETTFDSTVTTEVNGRT", "snv": [ { "evidence": [ { "id": "rs3905725", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3905725" }, { "id": "rs3905725", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs3905725" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SHS->NHS).", "chr_id": "12", "chr_pos": "78050095", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S709", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.690.690", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8IVL0-1.704.704", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.710.710", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.718.718", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.728.728", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.710.710", "start_pos": 710, "end_pos": 710, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2137229491", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137229491", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2137229491", "url": "https://www.ensembl.org/id/rs2137229491", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "ADLRQNLEETMSSLRGTQIS", "down_seq": "STLETTFDSTVTTEVNGRTI", "snv": [ { "evidence": [ { "id": "rs2137229491", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137229491" }, { "id": "rs2137229491", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2137229491" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HST->NST).", "chr_id": "12", "chr_pos": "78050097", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H710", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8IVL0-1.690.690", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.704.704", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.709.709", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q8IVL0-1.718.718", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8IVL0-1.728.728", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.718.718", "start_pos": 718, "end_pos": 718, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2137244792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137244792", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2137244792", "url": "https://www.ensembl.org/id/rs2137244792", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ETMSSLRGTQISHSTLETTF", "down_seq": "STVTTEVNGRTIPNLTSRPT", "snv": [ { "evidence": [ { "id": "rs2137244792", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137244792" }, { "id": "rs2137244792", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2137244792" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DST->NST).", "chr_id": "12", "chr_pos": "78050783", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D718", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q8IVL0-1.704.704", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.709.709", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8IVL0-1.710.710", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.728.728", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.728.728", "start_pos": 728, "end_pos": 728, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2137246456", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137246456", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2137246456", "url": "https://www.ensembl.org/id/rs2137246456", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1365767179", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1365767179", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1365767179", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1365767179", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ISHSTLETTFDSTVTTEVNG", "down_seq": "TIPNLTSRPTPMTWRLGQAC", "snv": [ { "evidence": [ { "id": "rs2137246456", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137246456" }, { "id": "rs2137246456", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2137246456" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGR->NGS).", "chr_id": "12", "chr_pos": "78050815", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R728", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1365767179", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1365767179" }, { "id": "rs1365767179", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1365767179" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGR->NGT).", "chr_id": "12", "chr_pos": "78050814", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R728", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.709.709", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q8IVL0-1.710.710", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.718.718", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.753.753", "start_pos": 753, "end_pos": 753, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LTSRPTPMTWRLGQACPRLQ", "down_seq": "GDAPSLGAGYPRSGTSRFIH", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78050889", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A753", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q8IVL0-1.758.758", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.766.766", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.770.770", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.772.772", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.766.766", "start_pos": 766, "end_pos": 766, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1285342555", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1285342555", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1285342555", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1285342555#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1285342555", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1285342555", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1285342555", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1285342555", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QACPRLQAGDAPSLGAGYPR", "down_seq": "GTSRFIHTDPSRFMYTTPLR", "snv": [ { "evidence": [ { "id": "rs1285342555", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1285342555" }, { "id": "rs1285342555", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1285342555#frequency_tab" }, { "id": "rs1285342555", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1285342555" }, { "id": "rs1285342555", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1285342555" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SGT->NGT).", "chr_id": "12", "chr_pos": "78050928", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S766", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.753.753", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q8IVL0-1.758.758", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.770.770", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.772.772", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.781.781", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.783.783", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8IVL0-1.786.786", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.770.770", "start_pos": 770, "end_pos": 770, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RLQAGDAPSLGAGYPRSGTS", "down_seq": "FIHTDPSRFMYTTPLRRAAV", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "12", "chr_pos": "78050940", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R770", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.753.753", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8IVL0-1.758.758", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.766.766", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.772.772", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8IVL0-1.781.781", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.783.783", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8IVL0-1.786.786", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.787.787", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.772.772", "start_pos": 772, "end_pos": 772, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752330645", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752330645", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752330645", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752330645", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752330645", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752330645", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "QAGDAPSLGAGYPRSGTSRF", "down_seq": "HTDPSRFMYTTPLRRAAVSR", "snv": [ { "evidence": [ { "id": "rs752330645", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752330645" }, { "id": "rs752330645", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752330645" }, { "id": "rs752330645", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752330645" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IHT->NHT).", "chr_id": "12", "chr_pos": "78050946", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I772", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.753.753", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8IVL0-1.758.758", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.766.766", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.770.770", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8IVL0-1.781.781", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8IVL0-1.783.783", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8IVL0-1.786.786", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.787.787", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.781.781", "start_pos": 781, "end_pos": 781, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1255684194", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1255684194", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1255684194", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1255684194", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "AGYPRSGTSRFIHTDPSRFM", "down_seq": "TTPLRRAAVSRLGNMSQIDM", "snv": [ { "evidence": [ { "id": "rs1255684194", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1255684194" }, { "id": "rs1255684194", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1255684194" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YTT->NTT).", "chr_id": "12", "chr_pos": "78050972", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y781", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.766.766", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8IVL0-1.770.770", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.772.772", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.783.783", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8IVL0-1.786.786", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.787.787", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8IVL0-1.800.800", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.783.783", "start_pos": 783, "end_pos": 783, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YPRSGTSRFIHTDPSRFMYT", "down_seq": "PLRRAAVSRLGNMSQIDMSE", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78050979", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T783", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.766.766", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.770.770", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q8IVL0-1.772.772", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.781.781", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8IVL0-1.786.786", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.787.787", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.800.800", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.786.786", "start_pos": 786, "end_pos": 786, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SGTSRFIHTDPSRFMYTTPL", "down_seq": "RAAVSRLGNMSQIDMSEKAS", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "12", "chr_pos": "78050988", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R786", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8IVL0-1.766.766", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8IVL0-1.770.770", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8IVL0-1.772.772", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8IVL0-1.781.781", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8IVL0-1.783.783", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.787.787", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8IVL0-1.800.800", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8IVL0-1.804.804", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.787.787", "start_pos": 787, "end_pos": 787, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GTSRFIHTDPSRFMYTTPLR", "down_seq": "AAVSRLGNMSQIDMSEKASS", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "78050991", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R787", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.770.770", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.772.772", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.781.781", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.783.783", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.786.786", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.800.800", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.804.804", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.800.800", "start_pos": 800, "end_pos": 800, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2137258757", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137258757", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2137258757", "url": "https://www.ensembl.org/id/rs2137258757", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MYTTPLRRAAVSRLGNMSQI", "down_seq": "MSEKASSDLDMSSEVDVGGY", "snv": [ { "evidence": [ { "id": "rs2137258757", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137258757" }, { "id": "rs2137258757", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2137258757" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DMS->NMS).", "chr_id": "12", "chr_pos": "78051029", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D800", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8IVL0-1.781.781", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.783.783", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8IVL0-1.786.786", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8IVL0-1.787.787", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.804.804", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.810.810", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8IVL0-1.820.820", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.804.804", "start_pos": 804, "end_pos": 804, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2137259552", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137259552", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2137259552", "url": "https://www.ensembl.org/id/rs2137259552", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PLRRAAVSRLGNMSQIDMSE", "down_seq": "ASSDLDMSSEVDVGGYMSDG", "snv": [ { "evidence": [ { "id": "rs2137259552", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137259552" }, { "id": "rs2137259552", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2137259552" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KAS->NAS).", "chr_id": "12", "chr_pos": "78051043", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K804", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8IVL0-1.786.786", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.787.787", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.800.800", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.810.810", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8IVL0-1.820.820", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.810.810", "start_pos": 810, "end_pos": 810, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs188997476", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188997476", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs188997476", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188997476", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs188997476", "url": "https://www.ncbi.nlm.nih.gov/snp/rs188997476#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs188997476", "url": "http://gnomad.broadinstitute.org/awesome?query=rs188997476", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VSRLGNMSQIDMSEKASSDL", "down_seq": "MSSEVDVGGYMSDGDILGKS", "snv": [ { "evidence": [ { "id": "rs188997476", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188997476" }, { "id": "rs188997476", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188997476" }, { "id": "rs188997476", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs188997476#frequency_tab" }, { "id": "rs188997476", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs188997476" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DMS->NMS).", "chr_id": "12", "chr_pos": "78051059", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D810", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.800.800", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q8IVL0-1.804.804", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.820.820", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.820.820", "start_pos": 820, "end_pos": 820, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2137262079", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137262079", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2137262079", "url": "https://www.ensembl.org/id/rs2137262079", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DMSEKASSDLDMSSEVDVGG", "down_seq": "MSDGDILGKSLRTDDINSGY", "snv": [ { "evidence": [ { "id": "rs2137262079", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137262079" }, { "id": "rs2137262079", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2137262079" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YMS->NMS).", "chr_id": "12", "chr_pos": "78051089", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y820", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8IVL0-1.800.800", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q8IVL0-1.804.804", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.810.810", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8IVL0-1.840.840", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.840.840", "start_pos": 840, "end_pos": 840, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2137404430", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137404430", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2137404430", "url": "https://www.ensembl.org/id/rs2137404430", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "YMSDGDILGKSLRTDDINSG", "down_seq": "MTDGGLNLYTRSLNRIPDTA", "snv": [ { "evidence": [ { "id": "rs2137404430", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2137404430" }, { "id": "rs2137404430", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2137404430" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YMT->NMT).", "chr_id": "12", "chr_pos": "78058997", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y840", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8IVL0-1.820.820", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.850.850", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.850.850", "start_pos": 850, "end_pos": 850, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1883917135", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1883917135", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1883917135", "url": "https://www.ensembl.org/id/rs1883917135", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SLRTDDINSGYMTDGGLNLY", "down_seq": "RSLNRIPDTATSRDIIQRGV", "snv": [ { "evidence": [ { "id": "rs1883917135", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1883917135" }, { "id": "rs1883917135", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1883917135" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TRS->NRS).", "chr_id": "12", "chr_pos": "78059028", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T850", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.840.840", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.85.85", "start_pos": 85, "end_pos": 85, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GEKKPLQGKAKEKEDSKIYT", "down_seq": "WANHYLAKSGHKRLIKDLQQ", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "D", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "12", "chr_pos": "77940330", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "D85", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q8IVL0-1.90.90", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.881.881", "start_pos": 881, "end_pos": 881, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1252410359", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1252410359", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1252410359", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1252410359#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1252410359", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1252410359", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TSRDIIQRGVHDVTVDADSW", "down_seq": "DSSSVSSGLSDTLDNISTDD", "snv": [ { "evidence": [ { "id": "rs1252410359", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1252410359" }, { "id": "rs1252410359", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1252410359#frequency_tab" }, { "id": "rs1252410359", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1252410359" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DDS->NDS).", "chr_id": "12", "chr_pos": "78116776", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D881", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8IVL0-1.872.872", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.882.882", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8IVL0-1.883.883", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8IVL0-1.897.897", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.882.882", "start_pos": 882, "end_pos": 882, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs375141185", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375141185", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs375141185", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375141185", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs375141185", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375141185", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SRDIIQRGVHDVTVDADSWD", "down_seq": "SSSVSSGLSDTLDNISTDDL", "snv": [ { "evidence": [ { "id": "rs375141185", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375141185" }, { "id": "rs375141185", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375141185" }, { "id": "rs375141185", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375141185" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DSS->NSS).", "chr_id": "12", "chr_pos": "78116779", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D882", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.872.872", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.881.881", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8IVL0-1.883.883", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.897.897", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.883.883", "start_pos": 883, "end_pos": 883, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs368822889", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368822889", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs368822889", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368822889", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs368822889", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368822889#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs368822889", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368822889", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RDIIQRGVHDVTVDADSWDD", "down_seq": "SSVSSGLSDTLDNISTDDLN", "snv": [ { "evidence": [ { "id": "rs368822889", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368822889" }, { "id": "rs368822889", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368822889" }, { "id": "rs368822889", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368822889#frequency_tab" }, { "id": "rs368822889", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368822889" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SSS->NSS).", "chr_id": "12", "chr_pos": "78116783", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S883", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8IVL0-1.872.872", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q8IVL0-1.881.881", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8IVL0-1.882.882", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8IVL0-1.897.897", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.897.897", "start_pos": 897, "end_pos": 897, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138517141", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138517141", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138517141", "url": "https://www.ensembl.org/id/rs2138517141", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "ADSWDDSSSVSSGLSDTLDN", "down_seq": "STDDLNTTSSVSSYSNITVP", "snv": [ { "evidence": [ { "id": "rs2138517141", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138517141" }, { "id": "rs2138517141", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138517141" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IST->NST).", "chr_id": "12", "chr_pos": "78116825", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I897", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8IVL0-1.881.881", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.882.882", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8IVL0-1.883.883", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.90.90", "start_pos": 90, "end_pos": 90, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1889748304", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1889748304", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1889748304", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1889748304#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LQGKAKEKEDSKIYTDWANH", "down_seq": "LAKSGHKRLIKDLQQDIADG", "snv": [ { "evidence": [ { "id": "rs1889748304", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1889748304" }, { "id": "rs1889748304", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1889748304#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NHY->NHC).", "chr_id": "12", "chr_pos": "77940344", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y90", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q8IVL0-1.85.85", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.920.920", "start_pos": 920, "end_pos": 920, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138521090", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138521090", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138521090", "url": "https://www.ensembl.org/id/rs2138521090", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "DDLNTTSSVSSYSNITVPSR", "down_seq": "NTQLRTDSEKRSTTDETWDS", "snv": [ { "evidence": [ { "id": "rs2138521090", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138521090" }, { "id": "rs2138521090", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138521090" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KNT->NNT).", "chr_id": "12", "chr_pos": "78116895", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K920", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.930.930", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8IVL0-1.935.935", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.930.930", "start_pos": 930, "end_pos": 930, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138562531", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138562531", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138562531", "url": "https://www.ensembl.org/id/rs2138562531", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SYSNITVPSRKNTQLRTDSE", "down_seq": "RSTTDETWDSPEELKKPEED", "snv": [ { "evidence": [ { "id": "rs2138562531", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138562531" }, { "id": "rs2138562531", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138562531" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KRS->NRS).", "chr_id": "12", "chr_pos": "78118047", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K930", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q8IVL0-1.920.920", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8IVL0-1.935.935", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.947.947", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.935.935", "start_pos": 935, "end_pos": 935, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2138563330", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138563330", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2138563330", "url": "https://www.ensembl.org/id/rs2138563330", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2138563330", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2138563330", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TVPSRKNTQLRTDSEKRSTT", "down_seq": "ETWDSPEELKKPEEDFDSHG", "snv": [ { "evidence": [ { "id": "rs2138563330", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2138563330" }, { "id": "rs2138563330", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2138563330" }, { "id": "rs2138563330", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2138563330" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DET->NET).", "chr_id": "12", "chr_pos": "78118060", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D935", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8IVL0-1.920.920", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8IVL0-1.930.930", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8IVL0-1.947.947", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.947.947", "start_pos": 947, "end_pos": 947, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "DSEKRSTTDETWDSPEELKK", "down_seq": "EEDFDSHGDAGGKWKTVSSG", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "12", "chr_pos": "78118096", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P947", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q8IVL0-1.930.930", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8IVL0-1.935.935", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.978.978", "start_pos": 978, "end_pos": 978, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8IVL0", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1269322414", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1269322414", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1269322414", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1269322414", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "GGKWKTVSSGLPEDPEKAGQ", "down_seq": "ASLSVSQTGSWRRGMSAQGG", "snv": [ { "evidence": [ { "id": "Q8IVL0", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8IVL0" }, { "id": "rs1269322414", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1269322414" }, { "id": "rs1269322414", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1269322414" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KAS->NAS).", "chr_id": "12", "chr_pos": "78118191", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K978", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.982.982", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q8IVL0-1.984.984", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8IVL0-1.988.988", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8IVL0-1.1459.1459", "start_pos": 1459, "end_pos": 1459, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" }, { "database": "iPTMnet", "id": "Q8IVL0", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] } ], "crossref": [ { "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IVL0", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IVL0", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EGKEWLRSHSTGGLQDTGNQ", "down_seq": "PLVSPSAMSSSAAGKYHFSN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "Q8IVL0", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IVL0" } ], "site_lbl": "Ser1459" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8IVL0-1.1447.1447", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8IVL0-1.1463.1463", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q8IVL0-1.1476.1476", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8IVL0-1.1463.1463", "start_pos": 1463, "end_pos": 1463, "uniprot_canonical_ac": "Q8IVL0-1", "length": 2385, "uniprot_id": "NAV3_HUMAN", "protein_name": "Neuron navigator 3", "refseq_ac": "NP_001019554", "refseq_name": "neuron navigator 3 isoform 1", "gene_name": "NAV3", "gene_names_uniprotkb": "NAV3; KIAA0938; POMFIL1; STEERIN3", "gene_names_refseq": "NAV3; NEDSFB; POMFIL1; STEERIN3; unc53H3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation.", "journal": "Science signaling", "date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" }, { "database": "iPTMnet", "id": "Q8IVL0", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IVL0" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] } ], "crossref": [ { "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8IVL0", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IVL0", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "WLRSHSTGGLQDTGNQSPLV", "down_seq": "PSAMSSSAAGKYHFSNLVSP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8IVL0", "url": "https://www.uniprot.org/uniprotkb/Q8IVL0" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "Q8IVL0", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8IVL0" } ], "site_lbl": "Ser1463" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "snv", "site_list": [ { "start_pos": "333", "end_pos": "333" }, { "start_pos": "872", "end_pos": "872" }, { "start_pos": "984", "end_pos": "984" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1030", "end_pos": "1030" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1060", "end_pos": "1060" }, { "start_pos": "1062", "end_pos": "1062" }, { "start_pos": "1079", "end_pos": "1079" }, { "start_pos": "1080", "end_pos": "1080" }, { "start_pos": "1085", "end_pos": "1085" }, { "start_pos": "1088", "end_pos": "1088" }, { "start_pos": "1100", "end_pos": "1100" }, { "start_pos": "1111", "end_pos": "1111" }, { "start_pos": "1115", "end_pos": "1115" }, { "start_pos": "1130", "end_pos": "1130" }, { "start_pos": "1135", "end_pos": "1135" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1158", "end_pos": "1158" }, { "start_pos": "1159", "end_pos": "1159" }, { "start_pos": "1162", "end_pos": "1162" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1184", "end_pos": "1184" }, { "start_pos": "1207", "end_pos": "1207" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1211", "end_pos": "1211" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "1226", "end_pos": "1226" }, { "start_pos": "1243", "end_pos": "1243" }, { "start_pos": "1249", "end_pos": "1249" }, { "start_pos": "1270", "end_pos": "1270" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "1305", "end_pos": "1305" }, { "start_pos": "1307", "end_pos": "1307" }, { "start_pos": "1315", "end_pos": "1315" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1324", "end_pos": "1324" }, { "start_pos": "1326", "end_pos": "1326" }, { "start_pos": "1333", "end_pos": "1333" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "1351", "end_pos": "1351" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1363", "end_pos": "1363" }, { "start_pos": "1383", "end_pos": "1383" }, { "start_pos": "1392", "end_pos": "1392" }, { "start_pos": "1403", "end_pos": "1403" }, { "start_pos": "1409", "end_pos": "1409" }, { "start_pos": "1447", "end_pos": "1447" }, { "start_pos": "1476", "end_pos": "1476" }, { "start_pos": "1492", "end_pos": "1492" }, { "start_pos": "1493", "end_pos": "1493" }, { "start_pos": "1495", "end_pos": "1495" }, { "start_pos": "1510", "end_pos": "1510" }, { "start_pos": "1534", "end_pos": "1534" }, { "start_pos": "1554", "end_pos": "1554" }, { "start_pos": "1559", "end_pos": "1559" }, { "start_pos": "1564", "end_pos": "1564" }, { "start_pos": "1575", "end_pos": "1575" }, { "start_pos": "1587", "end_pos": "1587" }, { "start_pos": "1612", "end_pos": "1612" }, { "start_pos": "1615", "end_pos": "1615" }, { "start_pos": "1655", "end_pos": "1655" }, { "start_pos": "1663", "end_pos": "1663" }, { "start_pos": "1668", "end_pos": "1668" }, { "start_pos": "1672", "end_pos": "1672" }, { "start_pos": "1676", "end_pos": "1676" }, { "start_pos": "1678", "end_pos": "1678" }, { "start_pos": "1679", "end_pos": "1679" }, { "start_pos": "1682", "end_pos": "1682" }, { "start_pos": "1685", "end_pos": "1685" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1737", "end_pos": "1737" }, { "start_pos": "1741", "end_pos": "1741" }, { "start_pos": "1751", "end_pos": "1751" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "1815", "end_pos": "1815" }, { "start_pos": "1860", "end_pos": "1860" }, { "start_pos": "1871", "end_pos": "1871" }, { "start_pos": "1872", "end_pos": "1872" }, { "start_pos": "1873", "end_pos": "1873" }, { "start_pos": "1906", "end_pos": "1906" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "1969", "end_pos": "1969" }, { "start_pos": "1981", "end_pos": "1981" }, { "start_pos": "1983", "end_pos": "1983" }, { "start_pos": "1990", "end_pos": "1990" }, { "start_pos": "2012", "end_pos": "2012" }, { "start_pos": "2013", "end_pos": "2013" }, { "start_pos": "2025", "end_pos": "2025" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "2040", "end_pos": "2040" }, { "start_pos": "2058", "end_pos": "2058" }, { "start_pos": "2075", "end_pos": "2075" }, { "start_pos": "2093", "end_pos": "2093" }, { "start_pos": "2107", "end_pos": "2107" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "2141", "end_pos": "2141" }, { "start_pos": "2145", "end_pos": "2145" }, { "start_pos": "2173", "end_pos": "2173" }, { "start_pos": "2193", "end_pos": "2193" }, { "start_pos": "2206", "end_pos": "2206" }, { "start_pos": "2232", "end_pos": "2232" }, { "start_pos": "2235", "end_pos": "2235" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "2315", "end_pos": "2315" }, { "start_pos": "2367", "end_pos": "2367" }, { "start_pos": "2369", "end_pos": "2369" }, { "start_pos": "2378", "end_pos": "2378" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "433", "end_pos": "433" }, { "start_pos": "437", "end_pos": "437" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "477", "end_pos": "477" }, { "start_pos": "498", "end_pos": "498" }, { "start_pos": "502", "end_pos": "502" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "510", "end_pos": "510" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "540", "end_pos": "540" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "558", "end_pos": "558" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "575", "end_pos": "575" }, { "start_pos": "579", "end_pos": "579" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "659", "end_pos": "659" }, { "start_pos": "661", "end_pos": "661" }, { "start_pos": "663", "end_pos": "663" }, { "start_pos": "667", "end_pos": "667" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "704", "end_pos": "704" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "710", "end_pos": "710" }, { "start_pos": "718", "end_pos": "718" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "753", "end_pos": "753" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "766", "end_pos": "766" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "772", "end_pos": "772" }, { "start_pos": "781", "end_pos": "781" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "786", "end_pos": "786" }, { "start_pos": "787", "end_pos": "787" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "883", "end_pos": "883" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "920", "end_pos": "920" }, { "start_pos": "930", "end_pos": "930" }, { "start_pos": "935", "end_pos": "935" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "982", "end_pos": "982" }, { "start_pos": "988", "end_pos": "988" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1463", "end_pos": "1463" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8IVL0-1.1447.1447", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8IVL0-1.1459.1459", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8IVL0-1.1476.1476", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z553-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Studying the O-GlcNAcome of human placentas using banked tissue samples.", "journal": "Glycobiology", "date": "2024-01-22", "authors": "Luna Sarai, Malard Florian, Pereckas Michaela, Aoki Mayumi, Aoki Kazahiro, Olivier-Van Stichelen Stephanie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q7Z553", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z553" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7Z553", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z553", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TNIQRHQGGRYYCKAENGLG", "down_seq": "PAIKSIRVDVYYLDDPVVTV", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser118", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q7Z553", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7Z553" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z553-1.213.213", "start_pos": 213, "end_pos": 213, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FTQGETKILKLKNLRPQDYA", "down_seq": "YSCIASVRNVCNIPDKMVSF", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn213", "evidence": [ { "id": "Q7Z553", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q7Z553#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q7Z553-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q7Z553-1.227.227", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.237.237", "start_pos": 237, "end_pos": 237, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "IASVRNVCNIPDKMVSFRLS", "down_seq": "KTASPSIKLLVDDPIVVNPG", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn237", "evidence": [ { "id": "Q7Z553", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q7Z553#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q7Z553-1.227.227", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.434.434", "start_pos": 434, "end_pos": 434, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TYTCVASLKGGGISDISIDV", "down_seq": "ISSSTVPPNLTVPQEKSPLV", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn434", "evidence": [ { "id": "Q7Z553", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q7Z553#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q7Z553-1.414.414", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z553-1.436.436", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q7Z553-1.443.443", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q7Z553-1.445.445", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.443.443", "start_pos": 443, "end_pos": 443, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GGGISDISIDVNISSSTVPP", "down_seq": "LTVPQEKSPLVTREGDTIEL", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn443", "evidence": [ { "id": "Q7Z553", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q7Z553#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q7Z553-1.434.434", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q7Z553-1.436.436", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q7Z553-1.445.445", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.504.504", "start_pos": 504, "end_pos": 504, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "VAMPDGSMQMESYDGTLRIV", "down_seq": "VSREMSGMYRCQTSQYNGFN", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn504", "evidence": [ { "id": "Q7Z553", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q7Z553#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NVS->KVS).", "chr_id": "14", "chr_pos": "47035111", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N504", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q7Z553-1.506.506", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.610.610", "start_pos": 610, "end_pos": 610, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SQEYTEYAVKSLSNENYGVY", "down_seq": "CSIINEAGAGRCSFLVTGKA", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn610", "evidence": [ { "id": "Q7Z553", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q7Z553#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NCS->KCS).", "chr_id": "14", "chr_pos": "46957426", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N610", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q7Z553-1.617.617", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.703.703", "start_pos": 703, "end_pos": 703, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "WWEQEIKINGNIQKGELITY", "down_seq": "LTELIKPEAYEVRLTPLTKF", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn703", "evidence": [ { "id": "Q7Z553", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q7Z553#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.92.92", "start_pos": 92, "end_pos": 92, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "Data Submission", "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000888", "url": "http://data.glygen.org/GLY_000888", "database": "Data Submission", "categories": [ "Other" ] }, { "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "IRWTKTAGSASDRFQDSSVF", "down_seq": "ETLRITNIQRHQGGRYYCKA", "glycosylation": [ { "glytoucan_ac": "G23719VF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FQDSSVFnETLR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn92", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G35029YA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FQDSSVFnETLR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn92", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G41071NU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FQDSSVFnETLR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn92", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G42124LM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FQDSSVFnETLR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn92", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G65184UU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FQDSSVFnETLR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn92", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G72790NZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FQDSSVFnETLR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn92", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G76295SF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FQDSSVFnETLR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn92", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FQDSSVFNETLR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn92", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "G95177YH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FQDSSVFnETLR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn92", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn92", "evidence": [ { "id": "Q7Z553", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/Q7Z553#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 10 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 9 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 9 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 9 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 9 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 9 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q7Z553-1.215.215", "start_pos": 215, "end_pos": 215, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QGETKILKLKNLRPQDYANY", "down_seq": "CIASVRNVCNIPDKMVSFRL", "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NYS->NYN).", "chr_id": "14", "chr_pos": "47131788", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S215", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q7Z553-1.213.213", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q7Z553-1.227.227", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.227.227", "start_pos": 227, "end_pos": 227, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "RPQDYANYSCIASVRNVCNI", "down_seq": "DKMVSFRLSNKTASPSIKLL", "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NIP->NIS).", "chr_id": "14", "chr_pos": "47131753", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P227", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q7Z553-1.213.213", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q7Z553-1.215.215", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q7Z553-1.237.237", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.322.322", "start_pos": 322, "end_pos": 322, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SDDAGTYSCIANNNVGNPAK", "down_seq": "STNIIVRALKKGRFWITPDP", "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KST->NST).", "chr_id": "14", "chr_pos": "47096876", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K322", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.378.378", "start_pos": 378, "end_pos": 378, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SCQVEAVPSEELTFSWFKNG", "down_seq": "PLRSSERMVITQTDPDVSPG", "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NGR->NGC).", "chr_id": "14", "chr_pos": "47061435", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R378", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.414.414", "start_pos": 414, "end_pos": 414, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DVSPGTTNLDIIDLKFTDFG", "down_seq": "YTCVASLKGGGISDISIDVN", "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "14", "chr_pos": "47061326", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T414", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "Q7Z553-1.434.434", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.436.436", "start_pos": 436, "end_pos": 436, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TCVASLKGGGISDISIDVNI", "down_seq": "SSTVPPNLTVPQEKSPLVTR", "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NIS->NIF).", "chr_id": "14", "chr_pos": "47061260", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S436", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q7Z553-1.434.434", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q7Z553-1.443.443", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q7Z553-1.445.445", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.445.445", "start_pos": 445, "end_pos": 445, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GISDISIDVNISSSTVPPNL", "down_seq": "VPQEKSPLVTREGDTIELQC", "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NLT->NLP).", "chr_id": "14", "chr_pos": "47035290", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "T445", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q7Z553-1.434.434", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q7Z553-1.436.436", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q7Z553-1.443.443", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.506.506", "start_pos": 506, "end_pos": 506, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MPDGSMQMESYDGTLRIVNV", "down_seq": "REMSGMYRCQTSQYNGFNVK", "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NVS->NVR).", "chr_id": "14", "chr_pos": "47061256", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S506", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NVS->NVY).", "chr_id": "14", "chr_pos": "47035106", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S506", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q7Z553-1.504.504", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.584.584", "start_pos": 584, "end_pos": 584, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LRAYPIRVLTYEWRLGNKLL", "down_seq": "TGQFDSQEYTEYAVKSLSNE", "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "14", "chr_pos": "46957506", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R584", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.617.617", "start_pos": 617, "end_pos": 617, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "AVKSLSNENYGVYNCSIINE", "down_seq": "GAGRCSFLVTGKAYAPEFYY", "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NEA->NET).", "chr_id": "14", "chr_pos": "46957407", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A617", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q7Z553-1.610.610", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.727.727", "start_pos": 727, "end_pos": 727, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LIKPEAYEVRLTPLTKFGEG", "down_seq": "STIRVIKYSAPVNPHLREFH", "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DST->NST).", "chr_id": "14", "chr_pos": "46882074", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D727", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q7Z553-1.731.731", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q7Z553-1.745.745", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.731.731", "start_pos": 731, "end_pos": 731, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EAYEVRLTPLTKFGEGDSTI", "down_seq": "VIKYSAPVNPHLREFHCGFE", "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "14", "chr_pos": "46882062", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R731", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q7Z553-1.727.727", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q7Z553-1.745.745", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.745.745", "start_pos": 745, "end_pos": 745, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "EGDSTIRVIKYSAPVNPHLR", "down_seq": "FHCGFEDGNICLFTQDDTDN", "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "14", "chr_pos": "46874198", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E745", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q7Z553-1.727.727", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q7Z553-1.731.731", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.845.845", "start_pos": 845, "end_pos": 845, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "KNPYGPTNTAYCFSFFYHMY", "down_seq": "QHIGVLNVYLRLKGQTTIEN", "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "G", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "14", "chr_pos": "46873444", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "G845", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.881.881", "start_pos": 881, "end_pos": 881, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TTIENPLWSSSGNKGQRWNE", "down_seq": "HVNIYPITSFQLIFEGIRGP", "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NEA->NES).", "chr_id": "14", "chr_pos": "46855059", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A881", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q7Z553-1.888.888", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q7Z553-1.899.899", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.888.888", "start_pos": 888, "end_pos": 888, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "WSSSGNKGQRWNEAHVNIYP", "down_seq": "TSFQLIFEGIRGPGIEGDIA", "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "I", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (ITS->NTS).", "chr_id": "14", "chr_pos": "46855037", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "I888", "disease": [ { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q7Z553-1.881.881", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q7Z553-1.899.899", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q7Z553-1.899.899", "start_pos": 899, "end_pos": 899, "uniprot_canonical_ac": "Q7Z553-1", "length": 956, "uniprot_id": "MDGA2_HUMAN", "protein_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2", "refseq_ac": "NP_878250", "refseq_name": "MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2", "gene_name": "MDGA2", "gene_names_uniprotkb": "MDGA2; MAMDC1; PRO23197", "gene_names_refseq": "MAMDC1; MDGA2; c14_5286", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7Z553", "url": "https://www.uniprot.org/uniprotkb/Q7Z553" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7Z553", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "NEAHVNIYPITSFQLIFEGI", "down_seq": "GPGIEGDIAIDDVSIAEGEC", "snv": [ { "evidence": [ { "id": "Q7Z553", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7Z553" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "14", "chr_pos": "46845853", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R899", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "213", "end_pos": "213" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "434", "end_pos": "434" }, { "start_pos": "443", "end_pos": "443" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "703", "end_pos": "703" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "snv", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "322", "end_pos": "322" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "414", "end_pos": "414" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "506", "end_pos": "506" }, { "start_pos": "584", "end_pos": "584" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "727", "end_pos": "727" }, { "start_pos": "731", "end_pos": "731" }, { "start_pos": "745", "end_pos": "745" }, { "start_pos": "845", "end_pos": "845" }, { "start_pos": "881", "end_pos": "881" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "899", "end_pos": "899" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q7Z553-1.881.881", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q7Z553-1.888.888", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8TAC9-1.136.136", "start_pos": 136, "end_pos": 136, "uniprot_canonical_ac": "Q8TAC9-1", "length": 235, "uniprot_id": "SCAM5_HUMAN", "protein_name": "Secretory carrier-associated membrane protein 5", "refseq_ac": "NP_001171582", "refseq_name": "secretory carrier-associated membrane protein 5", "gene_name": "SCAMP5", "gene_names_uniprotkb": "SCAMP5", "gene_names_refseq": "SCAMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8TAC9", "url": "https://www.uniprot.org/uniprotkb/Q8TAC9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8TAC9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8TAC9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LVISIIQAVGIPGWGVCGWI", "down_seq": "TISFFGTNIGSAVVMLIPTV", "snv": [ { "evidence": [ { "id": "Q8TAC9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8TAC9" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "75018429", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A136", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "60", "end_pos": "60" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8TAC9-1.168.168", "start_pos": 168, "end_pos": 168, "uniprot_canonical_ac": "Q8TAC9-1", "length": 235, "uniprot_id": "SCAM5_HUMAN", "protein_name": "Secretory carrier-associated membrane protein 5", "refseq_ac": "NP_001171582", "refseq_name": "secretory carrier-associated membrane protein 5", "gene_name": "SCAMP5", "gene_names_uniprotkb": "SCAMP5", "gene_names_refseq": "SCAMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8TAC9", "url": "https://www.uniprot.org/uniprotkb/Q8TAC9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8TAC9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8TAC9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "AVVMLIPTVMFTVMAVFSFI", "down_seq": "LSMVHKFYRGSGGSFSKAQE", "snv": [ { "evidence": [ { "id": "Q8TAC9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8TAC9" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "75018524", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A168", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "60", "end_pos": "60" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8TAC9-1.225.225", "start_pos": 225, "end_pos": 225, "uniprot_canonical_ac": "Q8TAC9-1", "length": 235, "uniprot_id": "SCAM5_HUMAN", "protein_name": "Secretory carrier-associated membrane protein 5", "refseq_ac": "NP_001171582", "refseq_name": "secretory carrier-associated membrane protein 5", "gene_name": "SCAMP5", "gene_names_uniprotkb": "SCAMP5", "gene_names_refseq": "SCAMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8TAC9", "url": "https://www.uniprot.org/uniprotkb/Q8TAC9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8TAC9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8TAC9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QNAAMGAAQGAMNQPQTQYS", "down_seq": "TPNYTYSNEM", "snv": [ { "evidence": [ { "id": "Q8TAC9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8TAC9" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "75018948", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A225", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "60", "end_pos": "60" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8TAC9-1.60.60", "start_pos": 60, "end_pos": 60, "uniprot_canonical_ac": "Q8TAC9-1", "length": 235, "uniprot_id": "SCAM5_HUMAN", "protein_name": "Secretory carrier-associated membrane protein 5", "refseq_ac": "NP_001171582", "refseq_name": "secretory carrier-associated membrane protein 5", "gene_name": "SCAMP5", "gene_names_uniprotkb": "SCAMP5", "gene_names_refseq": "SCAMP5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8TAC9", "url": "https://www.uniprot.org/uniprotkb/Q8TAC9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8TAC9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8TAC9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LYYLWMLNSVTLAVNLVGCL", "down_seq": "WLIGGGGATNFGLAFLWLIL", "snv": [ { "evidence": [ { "id": "Q8TAC9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8TAC9" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "75016634", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A60", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "Q8TAC9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8TAC9" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "15", "chr_pos": "75016635", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A60", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "136", "end_pos": "136" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "225", "end_pos": "225" }, { "start_pos": "60", "end_pos": "60" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.113.113", "start_pos": 113, "end_pos": 113, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs200305170", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200305170", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200305170", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200305170", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200305170", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200305170#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200305170", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200305170", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LALADFLYVLTLPALIFYYF", "down_seq": "KTDWIFGDAMCKLQRFIFHV", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn113", "evidence": [ { "id": "P47900", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P47900#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs200305170", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200305170" }, { "id": "rs200305170", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200305170" }, { "id": "rs200305170", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200305170#frequency_tab" }, { "id": "rs200305170", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200305170" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKT->SKT).", "chr_id": "3", "chr_pos": "152836120", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N113", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P47900-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P47900-1.110.110", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P47900-1.115.115", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.11.11", "start_pos": 11, "end_pos": 11, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P47900", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1021641035", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1021641035", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1021641035", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1021641035#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1021641035", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1021641035", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "MTEVLWPAVP", "down_seq": "GTDAAFLAGPGSSWGNSTVA", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn11", "evidence": [ { "id": "P47900", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P47900#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "P47900", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900" }, { "id": "rs1021641035", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1021641035" }, { "id": "rs1021641035", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1021641035#frequency_tab" }, { "id": "rs1021641035", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1021641035" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NGT->SGT).", "chr_id": "3", "chr_pos": "152835814", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N11", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P47900-1.13.13", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P47900-1.27.27", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P47900-1.29.29", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.197.197", "start_pos": 197, "end_pos": 197, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs750699440", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750699440", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750699440", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750699440", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750699440", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750699440#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LIVVVAISPILFYSGTGVRK", "down_seq": "KTITCYDTTSDEYLRSYFIY", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn197", "evidence": [ { "id": "P47900", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P47900#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs750699440", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750699440" }, { "id": "rs750699440", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750699440" }, { "id": "rs750699440", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750699440#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKT->KKT).", "chr_id": "3", "chr_pos": "152836373", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N197", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P47900-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P47900-1.203.203", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P47900-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P47900-1.205.205", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P47900-1.212.212", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.27.27", "start_pos": 27, "end_pos": 27, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs1576604048", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1576604048", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1576604048", "url": "https://www.ensembl.org/id/rs1576604048", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "PAVPNGTDAAFLAGPGSSWG", "down_seq": "STVASTAAVSSSFKCALTKT", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn27", "evidence": [ { "id": "P47900", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P47900#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs1576604048", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1576604048" }, { "id": "rs1576604048", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1576604048" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NST->DST).", "chr_id": "3", "chr_pos": "152835861", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N27", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P47900-1.11.11", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P47900-1.13.13", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P47900-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P47900-1.44.44", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Two disparate ligand-binding sites in the human P2Y1 receptor.", "journal": "Nature", "date": "2015", "authors": "Zhang D, Gao ZG, Zhang K, Kiselev E, Crane S, Wang J, Paoletta S, Yi C, Ma L, Zhang W, Han GW, Liu H, Cherezov V, Katritch V, Jiang H, Stevens RC, Jacobson KA, Zhao Q, Wu B", "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "reference": [ { "type": "PubMed", "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790" } ] } ], "crossref": [ { "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "MFNLALADFLYVLTLPALIF", "down_seq": "YFNKTDWIFGDAMCKLQRFI", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Loss of ADP analog binding.", "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" }, { "database": "PubMed", "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P47900-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P47900-1.113.113", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P47900-1.115.115", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P47900-1.203.203", "start_pos": 203, "end_pos": 203, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Two disparate ligand-binding sites in the human P2Y1 receptor.", "journal": "Nature", "date": "2015", "authors": "Zhang D, Gao ZG, Zhang K, Kiselev E, Crane S, Wang J, Paoletta S, Yi C, Ma L, Zhang W, Han GW, Liu H, Cherezov V, Katritch V, Jiang H, Stevens RC, Jacobson KA, Zhao Q, Wu B", "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "reference": [ { "type": "PubMed", "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790" } ] } ], "crossref": [ { "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "ISPILFYSGTGVRKNKTITC", "down_seq": "DTTSDEYLRSYFIYSMCTTV", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "A", "comment": "Loss of ADP analog binding.", "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" }, { "database": "PubMed", "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P47900-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P47900-1.197.197", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P47900-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P47900-1.205.205", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P47900-1.212.212", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P47900-1.205.205", "start_pos": 205, "end_pos": 205, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Two disparate ligand-binding sites in the human P2Y1 receptor.", "journal": "Nature", "date": "2015", "authors": "Zhang D, Gao ZG, Zhang K, Kiselev E, Crane S, Wang J, Paoletta S, Yi C, Ma L, Zhang W, Han GW, Liu H, Cherezov V, Katritch V, Jiang H, Stevens RC, Jacobson KA, Zhao Q, Wu B", "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "reference": [ { "type": "PubMed", "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790" } ] } ], "crossref": [ { "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PILFYSGTGVRKNKTITCYD", "down_seq": "TSDEYLRSYFIYSMCTTVAM", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "A", "comment": "Loss of ADP analog binding.", "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" }, { "database": "PubMed", "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P47900-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P47900-1.197.197", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P47900-1.203.203", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P47900-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P47900-1.212.212", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P47900-1.283.283", "start_pos": 283, "end_pos": 283, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Two disparate ligand-binding sites in the human P2Y1 receptor.", "journal": "Nature", "date": "2015", "authors": "Zhang D, Gao ZG, Zhang K, Kiselev E, Crane S, Wang J, Paoletta S, Yi C, Ma L, Zhang W, Han GW, Liu H, Cherezov V, Katritch V, Jiang H, Stevens RC, Jacobson KA, Zhao Q, Wu B", "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "reference": [ { "type": "PubMed", "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790" } ] } ], "crossref": [ { "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "IIVLTVFAVSYIPFHVMKTM", "down_seq": "LRARLDFQTPAMCAFNDRVY", "mutagenesis": [ { "sequence_org": "N", "sequence_mut": "A", "comment": "Loss of ADP analog binding.", "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" }, { "database": "PubMed", "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P47900-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P47900-1.301.301", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P47900-1.306.306", "start_pos": 306, "end_pos": 306, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Two disparate ligand-binding sites in the human P2Y1 receptor.", "journal": "Nature", "date": "2015", "authors": "Zhang D, Gao ZG, Zhang K, Kiselev E, Crane S, Wang J, Paoletta S, Yi C, Ma L, Zhang W, Han GW, Liu H, Cherezov V, Katritch V, Jiang H, Stevens RC, Jacobson KA, Zhao Q, Wu B", "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "reference": [ { "type": "PubMed", "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790" } ] } ], "crossref": [ { "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "ARLDFQTPAMCAFNDRVYAT", "down_seq": "QVTRGLASLNSCVDPILYFL", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Strongly decreased affinity for ADP analog.", "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" }, { "database": "PubMed", "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P47900-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P47900-1.304.304", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P47900-1.44.44", "start_pos": 44, "end_pos": 44, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Two disparate ligand-binding sites in the human P2Y1 receptor.", "journal": "Nature", "date": "2015", "authors": "Zhang D, Gao ZG, Zhang K, Kiselev E, Crane S, Wang J, Paoletta S, Yi C, Ma L, Zhang W, Han GW, Liu H, Cherezov V, Katritch V, Jiang H, Stevens RC, Jacobson KA, Zhao Q, Wu B", "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "reference": [ { "type": "PubMed", "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790" } ] } ], "crossref": [ { "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "SWGNSTVASTAAVSSSFKCA", "down_seq": "TKTGFQFYYLPAVYILVFII", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "A", "comment": "Loss of ADP analog binding.", "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" }, { "database": "PubMed", "id": "25822790", "url": "https://glygen.org/publication/PubMed/25822790" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P47900-1.27.27", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P47900-1.29.29", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P47900-1.115.115", "start_pos": 115, "end_pos": 115, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1252917102", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1252917102", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1252917102", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1252917102#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LADFLYVLTLPALIFYYFNK", "down_seq": "DWIFGDAMCKLQRFIFHVNL", "snv": [ { "evidence": [ { "id": "rs1252917102", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1252917102" }, { "id": "rs1252917102", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1252917102#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKT->NKI).", "chr_id": "3", "chr_pos": "152836126", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T115", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P47900-1.110.110", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P47900-1.113.113", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.136.136", "start_pos": 136, "end_pos": 136, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs779398688", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779398688", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779398688", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779398688", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779398688", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779398688#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779398688", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779398688", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs757564785", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757564785", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757564785", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757564785", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757564785", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757564785#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs757564785", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757564785", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DWIFGDAMCKLQRFIFHVNL", "down_seq": "GSILFLTCISAHRYSGVVYP", "snv": [ { "evidence": [ { "id": "rs779398688", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779398688" }, { "id": "rs779398688", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779398688" }, { "id": "rs779398688", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779398688#frequency_tab" }, { "id": "rs779398688", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779398688" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLY->NLC).", "chr_id": "3", "chr_pos": "152836189", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y136", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs757564785", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757564785" }, { "id": "rs757564785", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757564785" }, { "id": "rs757564785", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757564785#frequency_tab" }, { "id": "rs757564785", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757564785" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YGS->NGS).", "chr_id": "3", "chr_pos": "152836188", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y136", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.13.13", "start_pos": 13, "end_pos": 13, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P47900", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1185932281", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1185932281", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1185932281", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1185932281", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MTEVLWPAVPNG", "down_seq": "DAAFLAGPGSSWGNSTVAST", "snv": [ { "evidence": [ { "id": "P47900", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NGT->NGM).", "chr_id": "3", "chr_pos": "152835820", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T13", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1185932281", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1185932281" }, { "id": "rs1185932281", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1185932281" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NGT->NGR).", "chr_id": "3", "chr_pos": "152835820", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T13", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P47900-1.11.11", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P47900-1.27.27", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P47900-1.29.29", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.162.162", "start_pos": 162, "end_pos": 162, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P47900", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LTCISAHRYSGVVYPLKSLG", "down_seq": "LKKKNAICISVLVWLIVVVA", "snv": [ { "evidence": [ { "id": "P47900", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "152836266", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R162", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P47900-1.168.168", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.168.168", "start_pos": 168, "end_pos": 168, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P47900", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "HRYSGVVYPLKSLGRLKKKN", "down_seq": "ICISVLVWLIVVVAISPILF", "snv": [ { "evidence": [ { "id": "P47900", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "3", "chr_pos": "152836285", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A168", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P47900-1.162.162", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.195.195", "start_pos": 195, "end_pos": 195, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P47900", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VWLIVVVAISPILFYSGTGV", "down_seq": "KNKTITCYDTTSDEYLRSYF", "snv": [ { "evidence": [ { "id": "P47900", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "3", "chr_pos": "152836366", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R195", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P47900-1.197.197", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P47900-1.203.203", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P47900-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P47900-1.205.205", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P47900-1.212.212", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.204.204", "start_pos": 204, "end_pos": 204, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P47900", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2108027122", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2108027122", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2108027122", "url": "https://www.ensembl.org/id/rs2108027122", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SPILFYSGTGVRKNKTITCY", "down_seq": "TTSDEYLRSYFIYSMCTTVA", "snv": [ { "evidence": [ { "id": "P47900", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900" }, { "id": "rs2108027122", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2108027122" }, { "id": "rs2108027122", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2108027122" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DTT->NTT).", "chr_id": "3", "chr_pos": "152836392", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D204", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P47900-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P47900-1.197.197", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P47900-1.203.203", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P47900-1.205.205", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P47900-1.212.212", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.212.212", "start_pos": 212, "end_pos": 212, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P47900", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TGVRKNKTITCYDTTSDEYL", "down_seq": "SYFIYSMCTTVAMFCVPLVL", "snv": [ { "evidence": [ { "id": "P47900", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "3", "chr_pos": "152836416", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R212", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P47900-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P47900-1.197.197", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P47900-1.203.203", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P47900-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P47900-1.205.205", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.250.250", "start_pos": 250, "end_pos": 250, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs759997738", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759997738", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759997738", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759997738", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759997738", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759997738#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs759997738", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759997738", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LVLILGCYGLIVRALIYKDL", "down_seq": "NSPLRRKSIYLVIIVLTVFA", "snv": [ { "evidence": [ { "id": "rs759997738", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759997738" }, { "id": "rs759997738", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759997738" }, { "id": "rs759997738", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759997738#frequency_tab" }, { "id": "rs759997738", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759997738" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DNS->NNS).", "chr_id": "3", "chr_pos": "152836530", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D250", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P47900-1.252.252", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P47900-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P47900-1.268.268", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.253.253", "start_pos": 253, "end_pos": 253, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P47900", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs756222432", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756222432", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756222432", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756222432", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756222432", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756222432", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ILGCYGLIVRALIYKDLDNS", "down_seq": "LRRKSIYLVIIVLTVFAVSY", "snv": [ { "evidence": [ { "id": "P47900", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900" }, { "id": "rs756222432", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756222432" }, { "id": "rs756222432", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756222432" }, { "id": "rs756222432", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756222432" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NSP->NSS).", "chr_id": "3", "chr_pos": "152836539", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P253", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P47900-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P47900-1.252.252", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P47900-1.268.268", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.268.268", "start_pos": 268, "end_pos": 268, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P47900", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "DLDNSPLRRKSIYLVIIVLT", "down_seq": "FAVSYIPFHVMKTMNLRARL", "snv": [ { "evidence": [ { "id": "P47900", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "152836584", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V268", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P47900-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P47900-1.252.252", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P47900-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P47900-1.283.283", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.29.29", "start_pos": 29, "end_pos": 29, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs771382074", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771382074", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771382074", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771382074", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771382074", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771382074#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771382074", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771382074", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VPNGTDAAFLAGPGSSWGNS", "down_seq": "VASTAAVSSSFKCALTKTGF", "snv": [ { "evidence": [ { "id": "rs771382074", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771382074" }, { "id": "rs771382074", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771382074" }, { "id": "rs771382074", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771382074#frequency_tab" }, { "id": "rs771382074", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771382074" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NST->NSM).", "chr_id": "3", "chr_pos": "152835868", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T29", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs771382074", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771382074" }, { "id": "rs771382074", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771382074" }, { "id": "rs771382074", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771382074#frequency_tab" }, { "id": "rs771382074", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771382074" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NST->NSR).", "chr_id": "3", "chr_pos": "152835868", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T29", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P47900-1.11.11", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P47900-1.13.13", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P47900-1.27.27", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P47900-1.44.44", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.301.301", "start_pos": 301, "end_pos": 301, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P47900", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1716168788", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1716168788", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1716168788", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1716168788#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TMNLRARLDFQTPAMCAFND", "down_seq": "VYATYQVTRGLASLNSCVDP", "snv": [ { "evidence": [ { "id": "P47900", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900" }, { "id": "rs1716168788", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1716168788" }, { "id": "rs1716168788", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1716168788#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NDR->NDS).", "chr_id": "3", "chr_pos": "152836685", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R301", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P47900-1.283.283", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P47900-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P47900-1.306.306", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.304.304", "start_pos": 304, "end_pos": 304, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P47900", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LRARLDFQTPAMCAFNDRVY", "down_seq": "TYQVTRGLASLNSCVDPILY", "snv": [ { "evidence": [ { "id": "P47900", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "152836693", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A304", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P47900-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P47900-1.306.306", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.327.327", "start_pos": 327, "end_pos": 327, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P47900", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QVTRGLASLNSCVDPILYFL", "down_seq": "GDTFRRRLSRATRKASRRSE", "snv": [ { "evidence": [ { "id": "P47900", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900" } ], "glycoeffect": [], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "152836762", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A327", "disease": [ { "disease_id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." }, "synonyms": [ { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "tumor of the Ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "A primary or metastatic malignant neoplasm involving the ovary. Most primary malignant ovarian neoplasms are either carcinomas (serous, mucinous, or endometrioid adenocarcinomas) or malignant germ cell tumors. Metastatic malignant neoplasms to the ovary include carcinomas, lymphomas, and melanomas." }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.356.356", "start_pos": 356, "end_pos": 356, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P47900", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SRATRKASRRSEANLQSKSE", "down_seq": "MTLNILPEFKQNGDTSL", "snv": [ { "evidence": [ { "id": "P47900", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P47900" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DMT->NMT).", "chr_id": "3", "chr_pos": "152836848", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D356", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P47900-1.352.352", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P47900-1.354.354", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.94.94", "start_pos": 94, "end_pos": 94, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760860385", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760860385", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760860385", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760860385", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760860385", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760860385", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "WMFVFHMKPWSGISVYMFNL", "down_seq": "LADFLYVLTLPALIFYYFNK", "snv": [ { "evidence": [ { "id": "rs760860385", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760860385" }, { "id": "rs760860385", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760860385" }, { "id": "rs760860385", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760860385" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLA->NLS).", "chr_id": "3", "chr_pos": "152836062", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A94", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760860385", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760860385" }, { "id": "rs760860385", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760860385" }, { "id": "rs760860385", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760860385" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLA->NLT).", "chr_id": "3", "chr_pos": "152836062", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A94", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "P47900-1.110.110", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P47900-1.113.113", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P47900-1.252.252", "start_pos": 252, "end_pos": 252, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Pin1 induces the ADP-induced migration of human dental pulp cells through P2Y1 stabilization.", "journal": "Oncotarget", "date": "2016", "authors": "Kim SA, Choi HS, Ahn SG", "evidence": [ { "database": "iPTMnet", "id": "P47900", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P47900" } ], "reference": [ { "type": "PubMed", "id": "27863418", "url": "https://glygen.org/publication/PubMed/27863418" } ] } ], "crossref": [ { "id": "P47900", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P47900", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "27863418", "url": "https://glygen.org/publication/PubMed/27863418", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LILGCYGLIVRALIYKDLDN", "down_seq": "PLRRKSIYLVIIVLTVFAVS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P47900", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P47900" }, { "database": "PubMed", "id": "27863418", "url": "https://glygen.org/publication/PubMed/27863418" } ], "site_lbl": "Ser252" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P47900-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P47900-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P47900-1.268.268", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P47900-1.352.352", "start_pos": 352, "end_pos": 352, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphoproteome of resting human platelets.", "journal": "J. Proteome Res.", "date": "2008", "authors": "Zahedi RP, Lewandrowski U, Wiesner J, Wortelkamp S, Moebius J, Schutz C, Walter U, Gambaryan S, Sickmann A", "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" }, { "database": "iPTMnet", "id": "P47900", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P47900" } ], "reference": [ { "type": "PubMed", "id": "18088087", "url": "https://glygen.org/publication/PubMed/18088087" } ] } ], "crossref": [ { "id": "P47900", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P47900", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18088087", "url": "https://glygen.org/publication/PubMed/18088087", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RRRLSRATRKASRRSEANLQ", "down_seq": "KSEDMTLNILPEFKQNGDTS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P47900", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P47900" }, { "database": "PubMed", "id": "18088087", "url": "https://glygen.org/publication/PubMed/18088087" } ], "site_lbl": "Ser352" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P47900-1.354.354", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P47900-1.356.356", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P47900-1.354.354", "start_pos": 354, "end_pos": 354, "uniprot_canonical_ac": "P47900-1", "length": 373, "uniprot_id": "P2RY1_HUMAN", "protein_name": "P2Y purinoceptor 1", "refseq_ac": "NP_002554", "refseq_name": "P2Y purinoceptor 1", "gene_name": "P2RY1", "gene_names_uniprotkb": "P2RY1", "gene_names_refseq": "P2RY1; P2Y1; SARCC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphoproteome of resting human platelets.", "journal": "J. Proteome Res.", "date": "2008", "authors": "Zahedi RP, Lewandrowski U, Wiesner J, Wortelkamp S, Moebius J, Schutz C, Walter U, Gambaryan S, Sickmann A", "evidence": [ { "database": "UniProtKB", "id": "P47900", "url": "https://www.uniprot.org/uniprotkb/P47900" }, { "database": "iPTMnet", "id": "P47900", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P47900" } ], "reference": [ { "type": "PubMed", "id": "18088087", "url": "https://glygen.org/publication/PubMed/18088087" } ] } ], "crossref": [ { "id": "P47900", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P47900", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18088087", "url": "https://glygen.org/publication/PubMed/18088087", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RLSRATRKASRRSEANLQSK", "down_seq": "EDMTLNILPEFKQNGDTSL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P47900", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P47900" }, { "database": "PubMed", "id": "18088087", "url": "https://glygen.org/publication/PubMed/18088087" } ], "site_lbl": "Ser354" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "27", "end_pos": "27" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "44", "end_pos": "44" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "94", "end_pos": "94" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "252", "end_pos": "252" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "354", "end_pos": "354" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P47900-1.352.352", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P47900-1.356.356", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P34949-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "P34949", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P34949" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "crossref": [ { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P34949", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "P34949", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P34949" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P34949-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P34949-1.274.274", "start_pos": 274, "end_pos": 274, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs766010024", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766010024", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs766010024", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766010024", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs766010024", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766010024#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs766010024", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766010024", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs766010024", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs766010024", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1555479351", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555479351", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2505828744", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505828744", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1567268668", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567268668", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "IYFLNLLTLKPGEAMFLEAN", "down_seq": "PHAYLKGDCVECMACSDNTV", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs766010024", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766010024" }, { "id": "rs766010024", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766010024" }, { "id": "rs766010024", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766010024#frequency_tab" }, { "id": "rs766010024", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766010024" }, { "id": "rs766010024", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs766010024" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74896301", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V274", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs1555479351", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555479351" }, { "id": "rs2505828744", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505828744" }, { "id": "rs1567268668", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567268668" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897046", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V274", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.100.100", "start_pos": 100, "end_pos": 100, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs763691280", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763691280", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763691280", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763691280", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763691280", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763691280#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs763691280", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763691280", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "DSLGSKVKDTFNGNLPFLFK", "down_seq": "LSVETPLSIQAHPNKELAEK", "snv": [ { "evidence": [ { "id": "rs763691280", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763691280" }, { "id": "rs763691280", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763691280" }, { "id": "rs763691280", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763691280#frequency_tab" }, { "id": "rs763691280", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763691280" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891533", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V100", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.101.101", "start_pos": 101, "end_pos": 101, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1353562948", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1353562948", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1353562948", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1353562948", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2505815561", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505815561", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "SLGSKVKDTFNGNLPFLFKV", "down_seq": "SVETPLSIQAHPNKELAEKL", "snv": [ { "evidence": [ { "id": "rs1353562948", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1353562948" }, { "id": "rs1353562948", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1353562948" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891535", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L101", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505815561", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505815561" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892677", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L101", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.102.102", "start_pos": 102, "end_pos": 102, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphomannose isomerase deficiency: a carbohydrate-deficient glycoprotein syndrome with hepatic-intestinal presentation.", "journal": "American journal of human genetics", "date": "1998", "authors": "Jaeken J, Matthijs G, Saudubray JM, Dionisi-Vici C, Bertini E, de Lonlay P, Henri H, Carchon H, Schollen E, Van Schaftingen E", "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" }, { "database": "Reactome", "id": "R-HSA-4043916", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-4043916" }, { "database": "dbSNP", "id": "rs104894494", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894494" }, { "database": "dbSNP", "id": "rs104894495", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894495" } ], "reference": [ { "type": "PubMed", "id": "9585601", "url": "https://glygen.org/publication/PubMed/9585601" } ] }, { "title": "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.", "journal": "Journal of proteomics", "date": "2014", "authors": "Bian Y, Song C, Cheng K, Dong M, Wang F, Huang J, Sun D, Wang L, Ye M, Zou H", "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" }, { "database": "iPTMnet", "id": "P34949", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P34949" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] } ], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs104894494", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894494", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs104894494", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894494", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs104894494", "url": "https://www.ncbi.nlm.nih.gov/snp/rs104894494#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs104894494", "url": "http://gnomad.broadinstitute.org/awesome?query=rs104894494", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "9585601", "url": "https://glygen.org/publication/PubMed/9585601", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs104894494", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs104894494", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P34949", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P34949", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LGSKVKDTFNGNLPFLFKVL", "down_seq": "VETPLSIQAHPNKELAEKLH", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74891539", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S102", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs104894494", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894494" }, { "id": "rs104894494", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894494" }, { "id": "rs104894494", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs104894494#frequency_tab" }, { "id": "rs104894494", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs104894494" }, { "id": "9585601", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/9585601" }, { "id": "rs104894494", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs104894494" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74891539", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S102", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "P34949", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P34949" } ], "site_lbl": "Ser102" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P34949-1.103.103", "start_pos": 103, "end_pos": 103, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1376428111", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1376428111", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1376428111", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1376428111", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "GSKVKDTFNGNLPFLFKVLS", "down_seq": "ETPLSIQAHPNKELAEKLHL", "snv": [ { "evidence": [ { "id": "rs1376428111", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1376428111" }, { "id": "rs1376428111", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1376428111" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891542", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V103", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.104.104", "start_pos": 104, "end_pos": 104, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1439270419", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1439270419", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1439270419", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1439270419#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2064726930", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064726930", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064726930", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064726930#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "SKVKDTFNGNLPFLFKVLSV", "down_seq": "TPLSIQAHPNKELAEKLHLQ", "snv": [ { "evidence": [ { "id": "rs1439270419", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1439270419" }, { "id": "rs1439270419", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1439270419#frequency_tab" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891544", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E104", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2064726930", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064726930" }, { "id": "rs2064726930", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064726930#frequency_tab" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891545", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E104", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.105.105", "start_pos": 105, "end_pos": 105, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs556978187", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs556978187", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs556978187", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs556978187", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs556978187", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs556978187", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs556978187", "url": "http://gnomad.broadinstitute.org/awesome?query=rs556978187", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KVKDTFNGNLPFLFKVLSVE", "down_seq": "PLSIQAHPNKELAEKLHLQA", "snv": [ { "evidence": [ { "id": "rs556978187", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs556978187" }, { "id": "rs556978187", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs556978187" }, { "id": "rs556978187", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs556978187" }, { "id": "rs556978187", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs556978187" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891548", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "T105", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.106.106", "start_pos": 106, "end_pos": 106, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs765621023", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765621023", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765621023", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765621023", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765621023", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765621023#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs765621023", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765621023", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs765621023", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs765621023", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs2064727065", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064727065", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064727065", "url": "https://www.ensembl.org/id/rs2064727065", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "VKDTFNGNLPFLFKVLSVET", "down_seq": "LSIQAHPNKELAEKLHLQAP", "snv": [ { "evidence": [ { "id": "rs765621023", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765621023" }, { "id": "rs765621023", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765621023" }, { "id": "rs765621023", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765621023#frequency_tab" }, { "id": "rs765621023", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765621023" }, { "id": "rs765621023", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs765621023" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892692", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P106", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs2064727065", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064727065" }, { "id": "rs2064727065", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064727065" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891550", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P106", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.107.107", "start_pos": 107, "end_pos": 107, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1332019894", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1332019894", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1332019894", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1332019894#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2064727120", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064727120", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "KDTFNGNLPFLFKVLSVETP", "down_seq": "SIQAHPNKELAEKLHLQAPQ", "snv": [ { "evidence": [ { "id": "rs1332019894", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1332019894" }, { "id": "rs1332019894", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1332019894#frequency_tab" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891554", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L107", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2064727120", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064727120" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891553", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L107", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.10.10", "start_pos": 10, "end_pos": 10, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753133485", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753133485", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753133485", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753133485", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753133485", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753133485", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MAAPRVFPL", "down_seq": "CAVQQYAWGKMGSNSEVARL", "snv": [ { "evidence": [ { "id": "rs753133485", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753133485" }, { "id": "rs753133485", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753133485" }, { "id": "rs753133485", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753133485" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890539", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S10", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs753133485", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753133485" }, { "id": "rs753133485", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753133485" }, { "id": "rs753133485", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753133485" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890539", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S10", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P34949-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs780285052", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780285052", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780285052", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780285052", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780285052", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780285052", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "NGNLPFLFKVLSVETPLSIQ", "down_seq": "HPNKELAEKLHLQAPQHYPD", "snv": [ { "evidence": [ { "id": "rs780285052", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780285052" }, { "id": "rs780285052", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780285052" }, { "id": "rs780285052", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780285052" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891566", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A111", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.112.112", "start_pos": 112, "end_pos": 112, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753928850", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753928850", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753928850", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753928850", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753928850", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753928850#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs753928850", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753928850", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2141197839", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141197839", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "GNLPFLFKVLSVETPLSIQA", "down_seq": "PNKELAEKLHLQAPQHYPDA", "snv": [ { "evidence": [ { "id": "rs753928850", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753928850" }, { "id": "rs753928850", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753928850" }, { "id": "rs753928850", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753928850#frequency_tab" }, { "id": "rs753928850", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753928850" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891569", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H112", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs753928850", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753928850" }, { "id": "rs753928850", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753928850" }, { "id": "rs753928850", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753928850#frequency_tab" }, { "id": "rs753928850", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753928850" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891569", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H112", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2141197839", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141197839" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891569_74891572", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H112", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.115.115", "start_pos": 115, "end_pos": 115, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1661886822", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1661886822", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1661886822", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1661886822#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PFLFKVLSVETPLSIQAHPN", "down_seq": "ELAEKLHLQAPQHYPDANHK", "snv": [ { "evidence": [ { "id": "rs1661886822", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1661886822" }, { "id": "rs1661886822", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1661886822#frequency_tab" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891573_74891576", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K115", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.116.116", "start_pos": 116, "end_pos": 116, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs995939840", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs995939840", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs995939840", "url": "http://gnomad.broadinstitute.org/awesome?query=rs995939840", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2141200280", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141200280", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "FLFKVLSVETPLSIQAHPNK", "down_seq": "LAEKLHLQAPQHYPDANHKP", "snv": [ { "evidence": [ { "id": "rs995939840", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs995939840" }, { "id": "rs995939840", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs995939840" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892663", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E116", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2141200280", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141200280" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893147_74893148", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E116", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.117.117", "start_pos": 117, "end_pos": 117, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs377074383", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377074383", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs377074383", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377074383", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs377074383", "url": "http://gnomad.broadinstitute.org/awesome?query=rs377074383", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "LFKVLSVETPLSIQAHPNKE", "down_seq": "AEKLHLQAPQHYPDANHKPE", "snv": [ { "evidence": [ { "id": "rs377074383", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377074383" }, { "id": "rs377074383", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377074383" }, { "id": "rs377074383", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs377074383" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892664", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L117", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1206748497", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1206748497", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1206748497", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1206748497", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "FKVLSVETPLSIQAHPNKEL", "down_seq": "EKLHLQAPQHYPDANHKPEM", "snv": [ { "evidence": [ { "id": "rs1206748497", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1206748497" }, { "id": "rs1206748497", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1206748497" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892668", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A118", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74892667", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A118", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.119.119", "start_pos": 119, "end_pos": 119, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2064744356", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064744356", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064744356", "url": "https://www.ensembl.org/id/rs2064744356", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2064744356", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2064744356", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "KVLSVETPLSIQAHPNKELA", "down_seq": "KLHLQAPQHYPDANHKPEMA", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74892672", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "E119", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs2064744356", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064744356" }, { "id": "rs2064744356", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064744356" }, { "id": "rs2064744356", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2064744356" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74892670", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E119", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.11.11", "start_pos": 11, "end_pos": 11, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064708840", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064708840", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064708840", "url": "https://www.ensembl.org/id/rs2064708840", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs758921571", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758921571", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758921571", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758921571", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758921571", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758921571", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "MAAPRVFPLS", "down_seq": "AVQQYAWGKMGSNSEVARLL", "snv": [ { "evidence": [ { "id": "rs2064708840", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064708840" }, { "id": "rs2064708840", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064708840" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890543", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C11", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs758921571", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758921571" }, { "id": "rs758921571", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758921571" }, { "id": "rs758921571", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758921571" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890542", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C11", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P34949-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.120.120", "start_pos": 120, "end_pos": 120, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1260900758", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1260900758", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1260900758", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1260900758#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1260900758", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1260900758", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1439024206", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1439024206", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1439024206", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1439024206#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1439024206", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1439024206", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VLSVETPLSIQAHPNKELAE", "down_seq": "LHLQAPQHYPDANHKPEMAI", "snv": [ { "evidence": [ { "id": "rs1260900758", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1260900758" }, { "id": "rs1260900758", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1260900758#frequency_tab" }, { "id": "rs1260900758", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1260900758" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892673", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K120", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1260900758", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1260900758" }, { "id": "rs1260900758", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1260900758#frequency_tab" }, { "id": "rs1260900758", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1260900758" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892673", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K120", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1439024206", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1439024206" }, { "id": "rs1439024206", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1439024206#frequency_tab" }, { "id": "rs1439024206", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1439024206" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892674", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K120", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.121.121", "start_pos": 121, "end_pos": 121, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2505815561", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505815561", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "LSVETPLSIQAHPNKELAEK", "down_seq": "HLQAPQHYPDANHKPEMAIA", "snv": [ { "evidence": [ { "id": "rs2505815561", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505815561" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892677", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L121", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.122.122", "start_pos": 122, "end_pos": 122, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1595817960", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1595817960", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1595817960", "url": "https://www.ensembl.org/id/rs1595817960", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2064744612", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064744612", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064744612", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064744612#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "SVETPLSIQAHPNKELAEKL", "down_seq": "LQAPQHYPDANHKPEMAIAL", "snv": [ { "evidence": [ { "id": "rs1595817960", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1595817960" }, { "id": "rs1595817960", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1595817960" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892680", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H122", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2064744612", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064744612" }, { "id": "rs2064744612", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064744612#frequency_tab" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892679", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H122", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.124.124", "start_pos": 124, "end_pos": 124, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs954591103", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs954591103", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs954591103", "url": "https://www.ncbi.nlm.nih.gov/snp/rs954591103#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2505815582", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505815582", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "ETPLSIQAHPNKELAEKLHL", "down_seq": "APQHYPDANHKPEMAIALTP", "snv": [ { "evidence": [ { "id": "rs954591103", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs954591103" }, { "id": "rs954591103", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs954591103#frequency_tab" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892686", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q124", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505815582", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505815582" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892685", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q124", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.125.125", "start_pos": 125, "end_pos": 125, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs755077601", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755077601", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs755077601", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755077601", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs755077601", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755077601", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TPLSIQAHPNKELAEKLHLQ", "down_seq": "PQHYPDANHKPEMAIALTPF", "snv": [ { "evidence": [ { "id": "rs755077601", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755077601" }, { "id": "rs755077601", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755077601" }, { "id": "rs755077601", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755077601" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892689", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A125", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs755077601", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755077601" }, { "id": "rs755077601", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755077601" }, { "id": "rs755077601", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755077601" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892689", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A125", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.126.126", "start_pos": 126, "end_pos": 126, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs765621023", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765621023", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765621023", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765621023", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765621023", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765621023#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs765621023", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765621023", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs765621023", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs765621023", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "PLSIQAHPNKELAEKLHLQA", "down_seq": "QHYPDANHKPEMAIALTPFQ", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs765621023", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765621023" }, { "id": "rs765621023", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765621023" }, { "id": "rs765621023", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765621023#frequency_tab" }, { "id": "rs765621023", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765621023" }, { "id": "rs765621023", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs765621023" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74892692", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P126", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.128.128", "start_pos": 128, "end_pos": 128, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1204655433", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1204655433", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1204655433", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1204655433#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1204655433", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1204655433", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2141200350", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141200350", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2141200350", "url": "https://www.ensembl.org/id/rs2141200350", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs151030809", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs151030809", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs151030809", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs151030809", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs151030809", "url": "https://www.ncbi.nlm.nih.gov/snp/rs151030809#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs151030809", "url": "http://gnomad.broadinstitute.org/awesome?query=rs151030809", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2505816957", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505816957", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "SIQAHPNKELAEKLHLQAPQ", "down_seq": "YPDANHKPEMAIALTPFQGL", "snv": [ { "evidence": [ { "id": "rs1204655433", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1204655433" }, { "id": "rs1204655433", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1204655433#frequency_tab" }, { "id": "rs1204655433", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1204655433" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893182", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H128", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2141200350", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141200350" }, { "id": "rs2141200350", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2141200350" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893183", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H128", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1204655433", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1204655433" }, { "id": "rs1204655433", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1204655433#frequency_tab" }, { "id": "rs1204655433", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1204655433" }, { "id": "rs151030809", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs151030809" }, { "id": "rs151030809", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs151030809" }, { "id": "rs151030809", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs151030809#frequency_tab" }, { "id": "rs151030809", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs151030809" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893182", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H128", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505816957", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505816957" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893180", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H128", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.129.129", "start_pos": 129, "end_pos": 129, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs887249336", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs887249336", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs887249336", "url": "https://www.ncbi.nlm.nih.gov/snp/rs887249336#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs887249336", "url": "http://gnomad.broadinstitute.org/awesome?query=rs887249336", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs907858042", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs907858042", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs907858042", "url": "https://www.ensembl.org/id/rs907858042", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "IQAHPNKELAEKLHLQAPQH", "down_seq": "PDANHKPEMAIALTPFQGLC", "snv": [ { "evidence": [ { "id": "rs887249336", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs887249336" }, { "id": "rs887249336", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs887249336#frequency_tab" }, { "id": "rs887249336", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs887249336" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892701", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y129", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs907858042", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs907858042" }, { "id": "rs907858042", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs907858042" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892700", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y129", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs887249336", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs887249336" }, { "id": "rs887249336", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs887249336#frequency_tab" }, { "id": "rs887249336", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs887249336" } ], "glycoeffect": [], "sequence_org": "Y", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892701", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y129", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.12.12", "start_pos": 12, "end_pos": 12, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1596440893", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1596440893", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1596440893", "url": "https://www.ensembl.org/id/rs1596440893", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "MAAPRVFPLSC", "down_seq": "VQQYAWGKMGSNSEVARLLA", "snv": [ { "evidence": [ { "id": "rs1596440893", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1596440893" }, { "id": "rs1596440893", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1596440893" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890605", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A12", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1596440893", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1596440893" }, { "id": "rs1596440893", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1596440893" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890605", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A12", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P34949-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.130.130", "start_pos": 130, "end_pos": 130, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201189076", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201189076", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201189076", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201189076", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201189076", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201189076", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201189076", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201189076", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs202119520", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202119520", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs202119520", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs202119520", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs202119520", "url": "https://www.ncbi.nlm.nih.gov/snp/rs202119520#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "QAHPNKELAEKLHLQAPQHY", "down_seq": "DANHKPEMAIALTPFQGLCG", "snv": [ { "evidence": [ { "id": "rs201189076", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201189076" }, { "id": "rs201189076", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201189076" }, { "id": "rs201189076", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201189076" }, { "id": "rs201189076", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201189076" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892704", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "P130", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs202119520", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202119520" }, { "id": "rs202119520", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs202119520" }, { "id": "rs202119520", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs202119520#frequency_tab" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892703", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "P130", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.131.131", "start_pos": 131, "end_pos": 131, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs566620411", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs566620411", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs566620411", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs566620411", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs566620411", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs566620411", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs566620411", "url": "https://www.ncbi.nlm.nih.gov/snp/rs566620411#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs566620411", "url": "http://gnomad.broadinstitute.org/awesome?query=rs566620411", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs566620411", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs566620411", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AHPNKELAEKLHLQAPQHYP", "down_seq": "ANHKPEMAIALTPFQGLCGF", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs566620411", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs566620411" }, { "id": "rs566620411", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs566620411" }, { "id": "rs566620411", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs566620411" }, { "id": "rs566620411", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs566620411#frequency_tab" }, { "id": "rs566620411", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs566620411" }, { "id": "rs566620411", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs566620411" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74892706", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D131", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.133.133", "start_pos": 133, "end_pos": 133, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1417319890", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1417319890", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1417319890", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1417319890#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "PNKELAEKLHLQAPQHYPDA", "down_seq": "HKPEMAIALTPFQGLCGFRP", "snv": [ { "evidence": [ { "id": "rs1417319890", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1417319890" }, { "id": "rs1417319890", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1417319890#frequency_tab" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892713", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N133", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1417319890", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1417319890" }, { "id": "rs1417319890", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1417319890#frequency_tab" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892713", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N133", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.136.136", "start_pos": 136, "end_pos": 136, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs781645082", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781645082", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781645082", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781645082", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781645082", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781645082", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ELAEKLHLQAPQHYPDANHK", "down_seq": "EMAIALTPFQGLCGFRPVEE", "snv": [ { "evidence": [ { "id": "rs781645082", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781645082" }, { "id": "rs781645082", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781645082" }, { "id": "rs781645082", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781645082" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892721", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P136", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.137.137", "start_pos": 137, "end_pos": 137, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "LAEKLHLQAPQHYPDANHKP", "down_seq": "MAIALTPFQGLCGFRPVEEI", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74892726", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E137", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74892724", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "E137", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.138.138", "start_pos": 138, "end_pos": 138, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphomannose isomerase deficiency: a carbohydrate-deficient glycoprotein syndrome with hepatic-intestinal presentation.", "journal": "American journal of human genetics", "date": "1998", "authors": "Jaeken J, Matthijs G, Saudubray JM, Dionisi-Vici C, Bertini E, de Lonlay P, Henri H, Carchon H, Schollen E, Van Schaftingen E", "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" }, { "database": "Reactome", "id": "R-HSA-4043916", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-4043916" }, { "database": "dbSNP", "id": "rs104894494", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894494" }, { "database": "dbSNP", "id": "rs104894495", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894495" } ], "reference": [ { "type": "PubMed", "id": "9585601", "url": "https://glygen.org/publication/PubMed/9585601" } ] } ], "crossref": [ { "id": "rs150217523", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150217523", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs150217523", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150217523", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs150217523", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150217523", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs150217523", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150217523#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs150217523", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150217523", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs104894495", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894495", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs104894495", "url": "https://www.ncbi.nlm.nih.gov/snp/rs104894495#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "9585601", "url": "https://glygen.org/publication/PubMed/9585601", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "AEKLHLQAPQHYPDANHKPE", "down_seq": "AIALTPFQGLCGFRPVEEIV", "snv": [ { "evidence": [ { "id": "rs150217523", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150217523" }, { "id": "rs150217523", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150217523" }, { "id": "rs150217523", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150217523" }, { "id": "rs150217523", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150217523#frequency_tab" }, { "id": "rs150217523", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150217523" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892729", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.00176609", "site_lbl": "M138", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs104894495", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894495" }, { "id": "rs104894495", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs104894495#frequency_tab" }, { "id": "9585601", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/9585601" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892728", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M138", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "M", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74892727", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "M138", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P34949-1.140.140", "start_pos": 140, "end_pos": 140, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs773678732", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773678732", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773678732", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773678732", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773678732", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773678732#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs773678732", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773678732", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs760208119", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760208119", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760208119", "url": "https://www.ensembl.org/id/rs760208119", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "KLHLQAPQHYPDANHKPEMA", "down_seq": "ALTPFQGLCGFRPVEEIVTF", "snv": [ { "evidence": [ { "id": "rs773678732", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773678732" }, { "id": "rs773678732", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773678732" }, { "id": "rs773678732", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773678732#frequency_tab" }, { "id": "rs773678732", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773678732" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892734", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I140", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs760208119", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760208119" }, { "id": "rs760208119", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs760208119" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892733", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I140", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.141.141", "start_pos": 141, "end_pos": 141, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LHLQAPQHYPDANHKPEMAI", "down_seq": "LTPFQGLCGFRPVEEIVTFL", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74892736", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A141", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.144.144", "start_pos": 144, "end_pos": 144, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs368931988", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368931988", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs368931988", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368931988#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs368931988", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368931988", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs555471556", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs555471556", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs555471556", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs555471556", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs555471556", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs555471556", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs555471556", "url": "https://www.ncbi.nlm.nih.gov/snp/rs555471556#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs555471556", "url": "http://gnomad.broadinstitute.org/awesome?query=rs555471556", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs555471556", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs555471556", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "QAPQHYPDANHKPEMAIALT", "down_seq": "FQGLCGFRPVEEIVTFLKKV", "snv": [ { "evidence": [ { "id": "rs368931988", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368931988" }, { "id": "rs368931988", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368931988#frequency_tab" }, { "id": "rs368931988", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368931988" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892746", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P144", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs368931988", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368931988" }, { "id": "rs368931988", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368931988#frequency_tab" }, { "id": "rs368931988", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs368931988" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892746", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P144", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs555471556", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs555471556" }, { "id": "rs555471556", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs555471556" }, { "id": "rs555471556", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs555471556" }, { "id": "rs555471556", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs555471556#frequency_tab" }, { "id": "rs555471556", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs555471556" }, { "id": "rs555471556", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs555471556" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74892745", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P144", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.145.145", "start_pos": 145, "end_pos": 145, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2505815744", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505815744", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "APQHYPDANHKPEMAIALTP", "down_seq": "QGLCGFRPVEEIVTFLKKVP", "snv": [ { "evidence": [ { "id": "rs2505815744", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505815744" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892747", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F145", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.146.146", "start_pos": 146, "end_pos": 146, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2505815768", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505815768", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2505815768", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2505815768", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "PQHYPDANHKPEMAIALTPF", "down_seq": "GLCGFRPVEEIVTFLKKVPE", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs2505815768", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505815768" }, { "id": "rs2505815768", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2505815768" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74892751", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Q146", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.149.149", "start_pos": 149, "end_pos": 149, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064746068", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064746068", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064746068", "url": "https://www.ensembl.org/id/rs2064746068", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "YPDANHKPEMAIALTPFQGL", "down_seq": "GFRPVEEIVTFLKKVPEFQF", "snv": [ { "evidence": [ { "id": "rs2064746068", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064746068" }, { "id": "rs2064746068", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064746068" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892760", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C149", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.14.14", "start_pos": 14, "end_pos": 14, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1382095161", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1382095161", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1382095161", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1382095161#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1382095161", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1382095161", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs150404817", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150404817", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs150404817", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150404817", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs150404817", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150404817", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs150404817", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150404817#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs150404817", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150404817", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "MAAPRVFPLSCAV", "down_seq": "QYAWGKMGSNSEVARLLASS", "snv": [ { "evidence": [ { "id": "rs1382095161", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1382095161" }, { "id": "rs1382095161", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1382095161#frequency_tab" }, { "id": "rs1382095161", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1382095161" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890552", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q14", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs150404817", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150404817" }, { "id": "rs150404817", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150404817" }, { "id": "rs150404817", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150404817" }, { "id": "rs150404817", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150404817#frequency_tab" }, { "id": "rs150404817", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150404817" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890551", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "Q14", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P34949-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs766458792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766458792", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs766458792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766458792", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs766458792", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766458792#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs766458792", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766458792", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs760519827", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760519827", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760519827", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760519827", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760519827", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760519827", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ANHKPEMAIALTPFQGLCGF", "down_seq": "PVEEIVTFLKKVPEFQFLIG", "snv": [ { "evidence": [ { "id": "rs766458792", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766458792" }, { "id": "rs766458792", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766458792" }, { "id": "rs766458792", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766458792#frequency_tab" }, { "id": "rs766458792", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766458792" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892770", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R152", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs766458792", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766458792" }, { "id": "rs766458792", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766458792" }, { "id": "rs766458792", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766458792#frequency_tab" }, { "id": "rs766458792", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766458792" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892770", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R152", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs766458792", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766458792" }, { "id": "rs766458792", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766458792" }, { "id": "rs766458792", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs766458792#frequency_tab" }, { "id": "rs766458792", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766458792" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892770", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R152", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs760519827", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760519827" }, { "id": "rs760519827", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760519827" }, { "id": "rs760519827", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760519827" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892769", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R152", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.133.133", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.155.155", "start_pos": 155, "end_pos": 155, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2505817193", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505817193", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064753355", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064753355", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064753355", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064753355#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs759745815", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759745815", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759745815", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759745815", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759745815", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759745815#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs759745815", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759745815", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "KPEMAIALTPFQGLCGFRPV", "down_seq": "EIVTFLKKVPEFQFLIGDEA", "snv": [ { "evidence": [ { "id": "rs2505817193", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505817193" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893263", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E155", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs2064753355", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064753355" }, { "id": "rs2064753355", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064753355#frequency_tab" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893265", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E155", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs759745815", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759745815" }, { "id": "rs759745815", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759745815" }, { "id": "rs759745815", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759745815#frequency_tab" }, { "id": "rs759745815", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759745815" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892778", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E155", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs759745815", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759745815" }, { "id": "rs759745815", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759745815" }, { "id": "rs759745815", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759745815#frequency_tab" }, { "id": "rs759745815", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759745815" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892778", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E155", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.156.156", "start_pos": 156, "end_pos": 156, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1595818118", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1595818118", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1595818118", "url": "https://www.ensembl.org/id/rs1595818118", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1251860671", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1251860671", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1251860671", "url": "https://www.ensembl.org/id/rs1251860671", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "PEMAIALTPFQGLCGFRPVE", "down_seq": "IVTFLKKVPEFQFLIGDEAA", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74892783", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E156", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1595818118", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1595818118" }, { "id": "rs1595818118", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1595818118" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892782", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E156", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1251860671", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1251860671" }, { "id": "rs1251860671", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1251860671" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892781", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E156", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.158.158", "start_pos": 158, "end_pos": 158, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs886051482", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs886051482", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs886051482", "url": "https://www.ncbi.nlm.nih.gov/snp/rs886051482#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs886051482", "url": "http://gnomad.broadinstitute.org/awesome?query=rs886051482", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1309358071", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1309358071", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1309358071", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1309358071#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "MAIALTPFQGLCGFRPVEEI", "down_seq": "TFLKKVPEFQFLIGDEAATH", "snv": [ { "evidence": [ { "id": "rs886051482", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs886051482" }, { "id": "rs886051482", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs886051482#frequency_tab" }, { "id": "rs886051482", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs886051482" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892787", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V158", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ] }, { "evidence": [ { "id": "rs1309358071", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1309358071" }, { "id": "rs1309358071", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1309358071#frequency_tab" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893272", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V158", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.159.159", "start_pos": 159, "end_pos": 159, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1595818133", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1595818133", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1595818133", "url": "https://www.ensembl.org/id/rs1595818133", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AIALTPFQGLCGFRPVEEIV", "down_seq": "FLKKVPEFQFLIGDEAATHL", "snv": [ { "evidence": [ { "id": "rs1595818133", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1595818133" }, { "id": "rs1595818133", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1595818133" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892791", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T159", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74892791", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "T159", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.15.15", "start_pos": 15, "end_pos": 15, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2505811178", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505811178", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371649838", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371649838", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371649838", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371649838#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2505811185", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505811185", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2505811190", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505811190", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "MAAPRVFPLSCAVQ", "down_seq": "YAWGKMGSNSEVARLLASSD", "snv": [ { "evidence": [ { "id": "rs2505811178", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505811178" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890553", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q15", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs371649838", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371649838" }, { "id": "rs371649838", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371649838#frequency_tab" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890555", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q15", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs2505811185", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505811185" }, { "id": "rs2505811190", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505811190" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890553_74890554insCTGGG", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q15", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P34949-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.160.160", "start_pos": 160, "end_pos": 160, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs765418768", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765418768", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765418768", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765418768", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765418768", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765418768", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2064746713", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064746713", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064746713", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064746713#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "IALTPFQGLCGFRPVEEIVT", "down_seq": "LKKVPEFQFLIGDEAATHLK", "snv": [ { "evidence": [ { "id": "rs765418768", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765418768" }, { "id": "rs765418768", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765418768" }, { "id": "rs765418768", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765418768" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892794", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F160", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2064746713", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064746713" }, { "id": "rs2064746713", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064746713#frequency_tab" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892793", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F160", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.162.162", "start_pos": 162, "end_pos": 162, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs758670102", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758670102", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758670102", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758670102", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758670102", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758670102", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LTPFQGLCGFRPVEEIVTFL", "down_seq": "KVPEFQFLIGDEAATHLKQT", "snv": [ { "evidence": [ { "id": "rs758670102", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758670102" }, { "id": "rs758670102", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758670102" }, { "id": "rs758670102", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758670102" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892800", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K162", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.163.163", "start_pos": 163, "end_pos": 163, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064746885", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064746885", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064746885", "url": "https://www.ensembl.org/id/rs2064746885", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "TPFQGLCGFRPVEEIVTFLK", "down_seq": "VPEFQFLIGDEAATHLKQTM", "snv": [ { "evidence": [ { "id": "rs2064746885", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064746885" }, { "id": "rs2064746885", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064746885" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892802", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K163", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.164.164", "start_pos": 164, "end_pos": 164, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064751347", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064751347", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064751347", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064751347#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2505816823", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505816823", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "PFQGLCGFRPVEEIVTFLKK", "down_seq": "PEFQFLIGDEAATHLKQTMS", "snv": [ { "evidence": [ { "id": "rs2064751347", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064751347" }, { "id": "rs2064751347", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064751347#frequency_tab" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893140", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V164", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505816823", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505816823" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893140", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V164", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.166.166", "start_pos": 166, "end_pos": 166, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2141200280", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141200280", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "QGLCGFRPVEEIVTFLKKVP", "down_seq": "FQFLIGDEAATHLKQTMSHD", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74893146", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E166", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs2141200280", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141200280" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893147_74893148", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E166", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.146.146", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.167.167", "start_pos": 167, "end_pos": 167, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064751388", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064751388", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064751388", "url": "https://www.ensembl.org/id/rs2064751388", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "GLCGFRPVEEIVTFLKKVPE", "down_seq": "QFLIGDEAATHLKQTMSHDS", "snv": [ { "evidence": [ { "id": "rs2064751388", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064751388" }, { "id": "rs2064751388", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064751388" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893149", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F167", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.168.168", "start_pos": 168, "end_pos": 168, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs764447061", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764447061", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764447061", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764447061", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764447061", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764447061", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "LCGFRPVEEIVTFLKKVPEF", "down_seq": "FLIGDEAATHLKQTMSHDSQ", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74893152", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Q168", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs764447061", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764447061" }, { "id": "rs764447061", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764447061" }, { "id": "rs764447061", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764447061" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893213", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q168", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.169.169", "start_pos": 169, "end_pos": 169, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs981236841", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs981236841", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs981236841", "url": "https://www.ncbi.nlm.nih.gov/snp/rs981236841#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs981236841", "url": "http://gnomad.broadinstitute.org/awesome?query=rs981236841", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "CGFRPVEEIVTFLKKVPEFQ", "down_seq": "LIGDEAATHLKQTMSHDSQA", "snv": [ { "evidence": [ { "id": "rs981236841", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs981236841" }, { "id": "rs981236841", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs981236841#frequency_tab" }, { "id": "rs981236841", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs981236841" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893155", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F169", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.149.149", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.16.16", "start_pos": 16, "end_pos": 16, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs749914784", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749914784", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs749914784", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749914784", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs749914784", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749914784#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs749914784", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749914784", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "MAAPRVFPLSCAVQQ", "down_seq": "AWGKMGSNSEVARLLASSDP", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs749914784", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749914784" }, { "id": "rs749914784", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749914784" }, { "id": "rs749914784", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749914784#frequency_tab" }, { "id": "rs749914784", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749914784" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Y", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74890557", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Y16", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs749914784", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749914784" }, { "id": "rs749914784", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749914784" }, { "id": "rs749914784", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749914784#frequency_tab" }, { "id": "rs749914784", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749914784" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890557", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y16", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Y", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74890556", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "Y16", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P34949-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.171.171", "start_pos": 171, "end_pos": 171, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064751518", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064751518", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064751518", "url": "https://www.ensembl.org/id/rs2064751518", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1227673380", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1227673380", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1227673380", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1227673380", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "FRPVEEIVTFLKKVPEFQFL", "down_seq": "GDEAATHLKQTMSHDSQAVA", "snv": [ { "evidence": [ { "id": "rs2064751518", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064751518" }, { "id": "rs2064751518", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064751518" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893161", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I171", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1227673380", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1227673380" }, { "id": "rs1227673380", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1227673380" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893162", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I171", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.172.172", "start_pos": 172, "end_pos": 172, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1312022883", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1312022883", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1312022883", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1312022883", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "RPVEEIVTFLKKVPEFQFLI", "down_seq": "DEAATHLKQTMSHDSQAVAS", "snv": [ { "evidence": [ { "id": "rs1312022883", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1312022883" }, { "id": "rs1312022883", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1312022883" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893165", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G172", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.173.173", "start_pos": 173, "end_pos": 173, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs769569870", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769569870", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769569870", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769569870", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769569870", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769569870", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "PVEEIVTFLKKVPEFQFLIG", "down_seq": "EAATHLKQTMSHDSQAVASS", "snv": [ { "evidence": [ { "id": "rs769569870", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769569870" }, { "id": "rs769569870", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769569870" }, { "id": "rs769569870", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769569870" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893167", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D173", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.174.174", "start_pos": 174, "end_pos": 174, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1200674107", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1200674107", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1200674107", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1200674107", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "VEEIVTFLKKVPEFQFLIGD", "down_seq": "AATHLKQTMSHDSQAVASSL", "snv": [ { "evidence": [ { "id": "rs1200674107", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1200674107" }, { "id": "rs1200674107", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1200674107" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893170", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E174", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.155.155", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.176.176", "start_pos": 176, "end_pos": 176, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs727504018", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs727504018", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs727504018", "url": "https://www.ncbi.nlm.nih.gov/snp/rs727504018#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs727504018", "url": "http://gnomad.broadinstitute.org/awesome?query=rs727504018", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1256364766", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1256364766", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1256364766", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1256364766#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1256364766", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1256364766", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs748290939", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748290939", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748290939", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748290939", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748290939", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748290939", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1262821524", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1262821524", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1262821524", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1262821524#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1262821524", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1262821524", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "EIVTFLKKVPEFQFLIGDEA", "down_seq": "THLKQTMSHDSQAVASSLQS", "snv": [ { "evidence": [ { "id": "rs727504018", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs727504018" }, { "id": "rs727504018", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs727504018#frequency_tab" }, { "id": "rs727504018", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs727504018" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896158", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A176", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1256364766", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1256364766" }, { "id": "rs1256364766", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1256364766#frequency_tab" }, { "id": "rs1256364766", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1256364766" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893177", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A176", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs748290939", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748290939" }, { "id": "rs748290939", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748290939" }, { "id": "rs748290939", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748290939" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896157", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A176", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1262821524", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1262821524" }, { "id": "rs1262821524", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1262821524#frequency_tab" }, { "id": "rs1262821524", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1262821524" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893176", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A176", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs727504018", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs727504018" }, { "id": "rs727504018", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs727504018#frequency_tab" }, { "id": "rs727504018", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs727504018" }, { "id": "rs1256364766", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1256364766" }, { "id": "rs1256364766", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1256364766#frequency_tab" }, { "id": "rs1256364766", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1256364766" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896158", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A176", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.177.177", "start_pos": 177, "end_pos": 177, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs771926521", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771926521", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771926521", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771926521#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771926521", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771926521", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IVTFLKKVPEFQFLIGDEAA", "down_seq": "HLKQTMSHDSQAVASSLQSC", "snv": [ { "evidence": [ { "id": "rs771926521", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771926521" }, { "id": "rs771926521", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771926521#frequency_tab" }, { "id": "rs771926521", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771926521" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893180", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T177", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.178.178", "start_pos": 178, "end_pos": 178, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1204655433", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1204655433", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1204655433", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1204655433#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1204655433", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1204655433", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2141200350", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141200350", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2141200350", "url": "https://www.ensembl.org/id/rs2141200350", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2505816957", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505816957", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "VTFLKKVPEFQFLIGDEAAT", "down_seq": "LKQTMSHDSQAVASSLQSCF", "snv": [ { "evidence": [ { "id": "rs1204655433", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1204655433" }, { "id": "rs1204655433", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1204655433#frequency_tab" }, { "id": "rs1204655433", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1204655433" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893182", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H178", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2141200350", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141200350" }, { "id": "rs2141200350", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2141200350" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893183", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H178", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1204655433", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1204655433" }, { "id": "rs1204655433", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1204655433#frequency_tab" }, { "id": "rs1204655433", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1204655433" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893182", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H178", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505816957", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505816957" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893180", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H178", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.158.158", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.179.179", "start_pos": 179, "end_pos": 179, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064751993", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064751993", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064751993", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064751993#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2064752036", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064752036", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064752036", "url": "https://www.ensembl.org/id/rs2064752036", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "TFLKKVPEFQFLIGDEAATH", "down_seq": "KQTMSHDSQAVASSLQSCFS", "snv": [ { "evidence": [ { "id": "rs2064751993", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064751993" }, { "id": "rs2064751993", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064751993#frequency_tab" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893185", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L179", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2064752036", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064752036" }, { "id": "rs2064752036", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064752036" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893186", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L179", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.17.17", "start_pos": 17, "end_pos": 17, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs960734346", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs960734346", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs960734346", "url": "https://www.ensembl.org/id/rs960734346", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "MAAPRVFPLSCAVQQY", "down_seq": "WGKMGSNSEVARLLASSDPL", "snv": [ { "evidence": [ { "id": "rs960734346", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs960734346" }, { "id": "rs960734346", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs960734346" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890559", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A17", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P34949-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.180.180", "start_pos": 180, "end_pos": 180, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "FLKKVPEFQFLIGDEAATHL", "down_seq": "QTMSHDSQAVASSLQSCFSH", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74893190", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K180", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.183.183", "start_pos": 183, "end_pos": 183, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2064752183", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064752183", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064752183", "url": "https://www.ensembl.org/id/rs2064752183", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2064752135", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064752135", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064752135", "url": "https://www.ensembl.org/id/rs2064752135", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "KVPEFQFLIGDEAATHLKQT", "down_seq": "SHDSQAVASSLQSCFSHLMK", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "M", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74893199", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "M183", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "M", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74893197", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "M183", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs2064752183", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064752183" }, { "id": "rs2064752183", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064752183" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "M", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74893198", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "M183", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs2064752135", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064752135" }, { "id": "rs2064752135", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064752135" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893197", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M183", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.163.163", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752287684", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752287684", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752287684", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752287684", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752287684", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752287684", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1223590506", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1223590506", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1223590506", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1223590506#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs886043207", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs886043207", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs886043207", "url": "https://www.ncbi.nlm.nih.gov/snp/rs886043207#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2064752264", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064752264", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064752264", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064752264#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2064752264", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064752264", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2505817175", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505817175", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VPEFQFLIGDEAATHLKQTM", "down_seq": "HDSQAVASSLQSCFSHLMKS", "snv": [ { "evidence": [ { "id": "rs752287684", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752287684" }, { "id": "rs752287684", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752287684" }, { "id": "rs752287684", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752287684" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893261", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S184", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs752287684", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752287684" }, { "id": "rs752287684", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752287684" }, { "id": "rs752287684", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752287684" }, { "id": "rs1223590506", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1223590506" }, { "id": "rs1223590506", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1223590506#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74893201", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S184", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs886043207", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs886043207" }, { "id": "rs886043207", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs886043207#frequency_tab" }, { "id": "rs2064752264", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064752264" }, { "id": "rs2064752264", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064752264#frequency_tab" }, { "id": "rs2064752264", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064752264" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893262", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S184", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1223590506", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1223590506" }, { "id": "rs1223590506", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1223590506#frequency_tab" } ], "glycoeffect": [], "sequence_org": "S", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893201", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S184", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505817175", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505817175" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893262_74893265", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S184", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.164.164", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.186.186", "start_pos": 186, "end_pos": 186, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs762911151", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762911151", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762911151", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762911151", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762911151", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762911151", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "EFQFLIGDEAATHLKQTMSH", "down_seq": "SQAVASSLQSCFSHLMKSEK", "snv": [ { "evidence": [ { "id": "rs762911151", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762911151" }, { "id": "rs762911151", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762911151" }, { "id": "rs762911151", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762911151" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893206", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D186", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.166.166", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.187.187", "start_pos": 187, "end_pos": 187, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs199568830", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199568830", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs199568830", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199568830#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2064752388", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064752388", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064752388", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064752388", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FQFLIGDEAATHLKQTMSHD", "down_seq": "QAVASSLQSCFSHLMKSEKK", "snv": [ { "evidence": [ { "id": "rs199568830", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199568830" }, { "id": "rs199568830", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199568830#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893210", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S187", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2064752388", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064752388" }, { "id": "rs2064752388", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064752388" } ], "glycoeffect": [], "sequence_org": "S", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893209", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S187", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.188.188", "start_pos": 188, "end_pos": 188, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs764447061", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764447061", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764447061", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764447061", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764447061", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764447061", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "QFLIGDEAATHLKQTMSHDS", "down_seq": "AVASSLQSCFSHLMKSEKKV", "snv": [ { "evidence": [ { "id": "rs764447061", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764447061" }, { "id": "rs764447061", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764447061" }, { "id": "rs764447061", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764447061" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893213", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q188", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.168.168", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.169.169", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.190.190", "start_pos": 190, "end_pos": 190, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs781158335", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781158335", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781158335", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781158335", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781158335", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781158335#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs781158335", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781158335", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1555478606", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555478606", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LIGDEAATHLKQTMSHDSQA", "down_seq": "ASSLQSCFSHLMKSEKKVVV", "snv": [ { "evidence": [ { "id": "rs781158335", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781158335" }, { "id": "rs781158335", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781158335" }, { "id": "rs781158335", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781158335#frequency_tab" }, { "id": "rs781158335", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781158335" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893278", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V190", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1555478606", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555478606" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893279", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V190", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.193.193", "start_pos": 193, "end_pos": 193, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs939320011", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs939320011", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs939320011", "url": "https://www.ncbi.nlm.nih.gov/snp/rs939320011#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DEAATHLKQTMSHDSQAVAS", "down_seq": "LQSCFSHLMKSEKKVVVEQL", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74893228", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S193", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs939320011", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs939320011" }, { "id": "rs939320011", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs939320011#frequency_tab" } ], "glycoeffect": [], "sequence_org": "S", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893227", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S193", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.194.194", "start_pos": 194, "end_pos": 194, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "EAATHLKQTMSHDSQAVASS", "down_seq": "QSCFSHLMKSEKKVVVEQLN", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74893230", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "L194", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.174.174", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.196.196", "start_pos": 196, "end_pos": 196, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs761968053", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761968053", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs761968053", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761968053", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs761968053", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761968053#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs761968053", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761968053", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ATHLKQTMSHDSQAVASSLQ", "down_seq": "CFSHLMKSEKKVVVEQLNLL", "snv": [ { "evidence": [ { "id": "rs761968053", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761968053" }, { "id": "rs761968053", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761968053" }, { "id": "rs761968053", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs761968053#frequency_tab" }, { "id": "rs761968053", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761968053" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893237", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S196", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.177.177", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.199.199", "start_pos": 199, "end_pos": 199, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2505817125", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505817125", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LKQTMSHDSQAVASSLQSCF", "down_seq": "HLMKSEKKVVVEQLNLLVKR", "snv": [ { "evidence": [ { "id": "rs2505817125", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505817125" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893243", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S199", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.19.19", "start_pos": 19, "end_pos": 19, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1282146791", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1282146791", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1282146791", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1282146791#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1282146791", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1282146791", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2505811218", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505811218", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "MAAPRVFPLSCAVQQYAW", "down_seq": "KMGSNSEVARLLASSDPLAQ", "snv": [ { "evidence": [ { "id": "rs1282146791", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1282146791" }, { "id": "rs1282146791", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1282146791#frequency_tab" }, { "id": "rs1282146791", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1282146791" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890565", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G19", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505811218", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505811218" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890566_74890575", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G19", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.1.1", "start_pos": 1, "end_pos": 1, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs528828174", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs528828174", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2505811218", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505811218", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1555478015", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555478015", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "", "down_seq": "AAPRVFPLSCAVQQYAWGKM", "snv": [ { "evidence": [ { "id": "rs528828174", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs528828174" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890074", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs2505811218", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505811218" }, { "id": "rs1555478015", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555478015" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890566_74890575", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P34949-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.200.200", "start_pos": 200, "end_pos": 200, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs750743532", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750743532", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750743532", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750743532", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750743532", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750743532#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs750743532", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750743532", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs767875252", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767875252", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767875252", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767875252", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767875252", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767875252", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "KQTMSHDSQAVASSLQSCFS", "down_seq": "LMKSEKKVVVEQLNLLVKRI", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74893248", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "H200", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs750743532", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750743532" }, { "id": "rs750743532", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750743532" }, { "id": "rs750743532", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750743532#frequency_tab" }, { "id": "rs750743532", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750743532" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893250", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H200", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs767875252", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767875252" }, { "id": "rs767875252", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767875252" }, { "id": "rs767875252", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767875252" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893249", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H200", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.201.201", "start_pos": 201, "end_pos": 201, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064752971", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064752971", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064752971", "url": "https://www.ensembl.org/id/rs2064752971", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "QTMSHDSQAVASSLQSCFSH", "down_seq": "MKSEKKVVVEQLNLLVKRIS", "snv": [ { "evidence": [ { "id": "rs2064752971", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064752971" }, { "id": "rs2064752971", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064752971" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893252", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L201", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs2064752971", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064752971" }, { "id": "rs2064752971", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064752971" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893252", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L201", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.202.202", "start_pos": 202, "end_pos": 202, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064753056", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064753056", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064753056", "url": "https://www.ensembl.org/id/rs2064753056", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "TMSHDSQAVASSLQSCFSHL", "down_seq": "KSEKKVVVEQLNLLVKRISQ", "snv": [ { "evidence": [ { "id": "rs2064753056", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064753056" }, { "id": "rs2064753056", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064753056" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893255", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M202", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.203.203", "start_pos": 203, "end_pos": 203, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs780400102", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780400102", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780400102", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780400102", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780400102", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780400102#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs780400102", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780400102", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "MSHDSQAVASSLQSCFSHLM", "down_seq": "SEKKVVVEQLNLLVKRISQQ", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74893257", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K203", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs780400102", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780400102" }, { "id": "rs780400102", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780400102" }, { "id": "rs780400102", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780400102#frequency_tab" }, { "id": "rs780400102", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780400102" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893259", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K203", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.183.183", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.204.204", "start_pos": 204, "end_pos": 204, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752287684", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752287684", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752287684", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752287684", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752287684", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752287684", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs886043207", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs886043207", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs886043207", "url": "https://www.ncbi.nlm.nih.gov/snp/rs886043207#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2505817175", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505817175", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SHDSQAVASSLQSCFSHLMK", "down_seq": "EKKVVVEQLNLLVKRISQQA", "snv": [ { "evidence": [ { "id": "rs752287684", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752287684" }, { "id": "rs752287684", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752287684" }, { "id": "rs752287684", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752287684" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893261", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S204", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs752287684", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752287684" }, { "id": "rs752287684", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752287684" }, { "id": "rs752287684", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752287684" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74893261", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S204", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs886043207", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs886043207" }, { "id": "rs886043207", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs886043207#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893262", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S204", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505817175", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505817175" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893262_74893265", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S204", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.205.205", "start_pos": 205, "end_pos": 205, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2505817193", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505817193", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064753355", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064753355", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064753355", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064753355#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "HDSQAVASSLQSCFSHLMKS", "down_seq": "KKVVVEQLNLLVKRISQQAA", "snv": [ { "evidence": [ { "id": "rs2505817193", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505817193" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893263", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E205", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs2064753355", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064753355" }, { "id": "rs2064753355", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064753355#frequency_tab" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893265", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E205", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.207.207", "start_pos": 207, "end_pos": 207, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs142123160", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142123160", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs142123160", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142123160", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs142123160", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142123160#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs142123160", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142123160", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs146006563", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146006563", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs146006563", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146006563", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs146006563", "url": "https://www.ncbi.nlm.nih.gov/snp/rs146006563#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs146006563", "url": "http://gnomad.broadinstitute.org/awesome?query=rs146006563", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SQAVASSLQSCFSHLMKSEK", "down_seq": "VVVEQLNLLVKRISQQAAAG", "snv": [ { "evidence": [ { "id": "rs142123160", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142123160" }, { "id": "rs142123160", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142123160" }, { "id": "rs142123160", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142123160#frequency_tab" }, { "id": "rs142123160", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142123160" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893269", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K207", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs146006563", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146006563" }, { "id": "rs146006563", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146006563" }, { "id": "rs146006563", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs146006563#frequency_tab" }, { "id": "rs146006563", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs146006563" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893270", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K207", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.187.187", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.208.208", "start_pos": 208, "end_pos": 208, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1309358071", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1309358071", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1309358071", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1309358071#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "QAVASSLQSCFSHLMKSEKK", "down_seq": "VVEQLNLLVKRISQQAAAGN", "snv": [ { "evidence": [ { "id": "rs1309358071", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1309358071" }, { "id": "rs1309358071", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1309358071#frequency_tab" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893272", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V208", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74893272", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V208", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.188.188", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.20.20", "start_pos": 20, "end_pos": 20, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064709333", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064709333", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064709333", "url": "https://www.ensembl.org/id/rs2064709333", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs779832985", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779832985", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779832985", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779832985", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779832985", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779832985#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779832985", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779832985", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "", "down_seq": "MGSNSEVARLLASSDPLAQI", "snv": [ { "evidence": [ { "id": "rs2064709333", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064709333" }, { "id": "rs2064709333", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064709333" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890568", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K20", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs779832985", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779832985" }, { "id": "rs779832985", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779832985" }, { "id": "rs779832985", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779832985#frequency_tab" }, { "id": "rs779832985", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779832985" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890570", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K20", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.210.210", "start_pos": 210, "end_pos": 210, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs781158335", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781158335", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781158335", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781158335", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781158335", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781158335#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs781158335", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781158335", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1555478606", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555478606", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "VASSLQSCFSHLMKSEKKVV", "down_seq": "EQLNLLVKRISQQAAAGNNM", "snv": [ { "evidence": [ { "id": "rs781158335", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781158335" }, { "id": "rs781158335", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781158335" }, { "id": "rs781158335", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781158335#frequency_tab" }, { "id": "rs781158335", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781158335" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893278", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V210", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1555478606", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555478606" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893279", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V210", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.190.190", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.211.211", "start_pos": 211, "end_pos": 211, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs769810913", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769810913", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769810913", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769810913", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769810913", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769810913#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs769810913", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769810913", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1374119101", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1374119101", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "ASSLQSCFSHLMKSEKKVVV", "down_seq": "QLNLLVKRISQQAAAGNNME", "snv": [ { "evidence": [ { "id": "rs769810913", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769810913" }, { "id": "rs769810913", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769810913" }, { "id": "rs769810913", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769810913#frequency_tab" }, { "id": "rs769810913", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769810913" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893281", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E211", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1374119101", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1374119101" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893281", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E211", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.212.212", "start_pos": 212, "end_pos": 212, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs775284878", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775284878", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775284878", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775284878", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775284878", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775284878", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "SSLQSCFSHLMKSEKKVVVE", "down_seq": "LNLLVKRISQQAAAGNNMED", "snv": [ { "evidence": [ { "id": "rs775284878", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775284878" }, { "id": "rs775284878", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775284878" }, { "id": "rs775284878", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775284878" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893284", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q212", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs775284878", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775284878" }, { "id": "rs775284878", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775284878" }, { "id": "rs775284878", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775284878" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893284", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q212", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.214.214", "start_pos": 214, "end_pos": 214, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1190823083", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1190823083", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1190823083", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1190823083", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs768635142", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768635142", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768635142", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768635142", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs768635142", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768635142", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LQSCFSHLMKSEKKVVVEQL", "down_seq": "LLVKRISQQAAAGNNMEDIF", "snv": [ { "evidence": [ { "id": "rs1190823083", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1190823083" }, { "id": "rs1190823083", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1190823083" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893291", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N214", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs768635142", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768635142" }, { "id": "rs768635142", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768635142" }, { "id": "rs768635142", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768635142" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893290", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N214", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.194.194", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.196.196", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.217.217", "start_pos": 217, "end_pos": 217, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs774351484", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774351484", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774351484", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774351484", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774351484", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774351484#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774351484", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774351484", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "CFSHLMKSEKKVVVEQLNLL", "down_seq": "KRISQQAAAGNNMEDIFGEL", "snv": [ { "evidence": [ { "id": "rs774351484", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774351484" }, { "id": "rs774351484", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774351484" }, { "id": "rs774351484", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774351484#frequency_tab" }, { "id": "rs774351484", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774351484" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893299", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V217", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs774351484", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774351484" }, { "id": "rs774351484", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774351484" }, { "id": "rs774351484", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774351484#frequency_tab" }, { "id": "rs774351484", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774351484" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893299", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V217", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.218.218", "start_pos": 218, "end_pos": 218, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1057516424", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057516424", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1057516424", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1057516424#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1057516424", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1057516424", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1173955006", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1173955006", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1173955006", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1173955006", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "FSHLMKSEKKVVVEQLNLLV", "down_seq": "RISQQAAAGNNMEDIFGELL", "snv": [ { "evidence": [ { "id": "rs1057516424", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057516424" }, { "id": "rs1057516424", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1057516424#frequency_tab" }, { "id": "rs1057516424", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1057516424" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893302", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K218", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1173955006", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1173955006" }, { "id": "rs1173955006", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1173955006" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893303", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K218", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74893304", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K218", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.219.219", "start_pos": 219, "end_pos": 219, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Genomic organization of the human phosphomannose isomerase (MPI) gene and mutation analysis in patients with congenital disorders of glycosylation type Ib (CDG-Ib).", "journal": "Human mutation", "date": "2000", "authors": "Schollen E, Dorland L, de Koning TJ, Van Diggelen OP, Huijmans JG, Marquardt T, Babovic-Vuksanovic D, Patterson M, Imtiaz F, Winchester B, Adamowicz M, Pronicka E, Freeze H, Matthijs G", "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" }, { "database": "Reactome", "id": "R-HSA-446205", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-446205" }, { "database": "dbSNP", "id": "rs104894489", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894489" }, { "database": "dbSNP", "id": "rs786204593", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs786204593" } ], "reference": [ { "type": "PubMed", "id": "10980531", "url": "https://glygen.org/publication/PubMed/10980531" } ] }, { "title": "Carbohydrate-deficient glycoprotein syndrome type Ib. Phosphomannose isomerase deficiency and mannose therapy.", "journal": "The Journal of clinical investigation", "date": "1998", "authors": "Niehues R, Hasilik M, Alton G, Korner C, Schiebe-Sukumar M, Koch HG, Zimmer KP, Wu R, Harms E, Reiter K, von Figura K, Freeze HH, Harms HK, Marquardt T", "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" }, { "database": "Reactome", "id": "R-HSA-4043916", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-4043916" }, { "database": "dbSNP", "id": "rs104894489", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894489" } ], "reference": [ { "type": "PubMed", "id": "9525984", "url": "https://glygen.org/publication/PubMed/9525984" } ] } ], "crossref": [ { "id": "rs104894489", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894489", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs104894489", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894489", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs104894489", "url": "https://www.ncbi.nlm.nih.gov/snp/rs104894489#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs104894489", "url": "http://gnomad.broadinstitute.org/awesome?query=rs104894489", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "10980531", "url": "https://glygen.org/publication/PubMed/10980531", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9525984", "url": "https://glygen.org/publication/PubMed/9525984", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs104894489", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs104894489", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs138891630", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138891630", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs138891630", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138891630", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs138891630", "url": "https://www.ncbi.nlm.nih.gov/snp/rs138891630#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs138891630", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138891630", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SHLMKSEKKVVVEQLNLLVK", "down_seq": "ISQQAAAGNNMEDIFGELLL", "snv": [ { "evidence": [ { "id": "rs104894489", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894489" }, { "id": "rs104894489", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894489" }, { "id": "rs104894489", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs104894489#frequency_tab" }, { "id": "rs104894489", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs104894489" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893306", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R219", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs104894489", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894489" }, { "id": "rs104894489", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894489" }, { "id": "rs104894489", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs104894489#frequency_tab" }, { "id": "rs104894489", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs104894489" }, { "id": "10980531", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/10980531" }, { "id": "9525984", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/9525984" }, { "id": "rs104894489", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs104894489" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74893306", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R219", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs138891630", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138891630" }, { "id": "rs138891630", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138891630" }, { "id": "rs138891630", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs138891630#frequency_tab" }, { "id": "rs138891630", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138891630" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893305", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R219", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.199.199", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P34949-1.21.21", "start_pos": 21, "end_pos": 21, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1471146448", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1471146448", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1471146448", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1471146448#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs778966484", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778966484", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778966484", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778966484", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778966484", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778966484", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs376746368", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376746368", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs376746368", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376746368", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs376746368", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376746368#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs376746368", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376746368", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "MAAPRVFPLSCAVQQYAWGK", "down_seq": "GSNSEVARLLASSDPLAQIA", "snv": [ { "evidence": [ { "id": "rs1471146448", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1471146448" }, { "id": "rs1471146448", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1471146448#frequency_tab" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890573", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M21", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs778966484", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778966484" }, { "id": "rs778966484", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778966484" }, { "id": "rs778966484", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778966484" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890572", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M21", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs778966484", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778966484" }, { "id": "rs778966484", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778966484" }, { "id": "rs778966484", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778966484" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890572", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M21", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs376746368", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376746368" }, { "id": "rs376746368", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376746368" }, { "id": "rs376746368", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376746368#frequency_tab" }, { "id": "rs376746368", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376746368" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890571", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M21", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.220.220", "start_pos": 220, "end_pos": 220, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064754424", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064754424", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "HLMKSEKKVVVEQLNLLVKR", "down_seq": "SQQAAAGNNMEDIFGELLLQ", "snv": [ { "evidence": [ { "id": "rs2064754424", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064754424" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893307", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I220", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.221.221", "start_pos": 221, "end_pos": 221, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760911969", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760911969", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760911969", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760911969", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760911969", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760911969#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs760911969", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760911969", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1202432300", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1202432300", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1202432300", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1202432300#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LMKSEKKVVVEQLNLLVKRI", "down_seq": "QQAAAGNNMEDIFGELLLQL", "snv": [ { "evidence": [ { "id": "rs760911969", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760911969" }, { "id": "rs760911969", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760911969" }, { "id": "rs760911969", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760911969#frequency_tab" }, { "id": "rs760911969", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760911969" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893312", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S221", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs760911969", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760911969" }, { "id": "rs760911969", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760911969" }, { "id": "rs760911969", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760911969#frequency_tab" }, { "id": "rs760911969", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760911969" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893312", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S221", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1202432300", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1202432300" }, { "id": "rs1202432300", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1202432300#frequency_tab" } ], "glycoeffect": [], "sequence_org": "S", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893311", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S221", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.201.201", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.202.202", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.223.223", "start_pos": 223, "end_pos": 223, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs749911553", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749911553", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs749911553", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749911553", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs749911553", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749911553", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2064815550", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064815550", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064815550", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064815550#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1296346165", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1296346165", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1296346165", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1296346165", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "KSEKKVVVEQLNLLVKRISQ", "down_seq": "AAAGNNMEDIFGELLLQLHQ", "snv": [ { "evidence": [ { "id": "rs749911553", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749911553" }, { "id": "rs749911553", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749911553" }, { "id": "rs749911553", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749911553" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896208", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q223", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs2064815550", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064815550" }, { "id": "rs2064815550", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064815550#frequency_tab" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896210", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q223", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1296346165", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1296346165" }, { "id": "rs1296346165", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1296346165" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74893318", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q223", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.224.224", "start_pos": 224, "end_pos": 224, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs768186349", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768186349", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs373222545", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373222545", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs373222545", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373222545", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs373222545", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373222545#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs373222545", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373222545", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SEKKVVVEQLNLLVKRISQQ", "down_seq": "AAGNNMEDIFGELLLQLHQQ", "snv": [ { "evidence": [ { "id": "rs768186349", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768186349" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "=", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896153", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A224", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs373222545", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373222545" }, { "id": "rs373222545", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373222545" }, { "id": "rs373222545", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373222545#frequency_tab" }, { "id": "rs373222545", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373222545" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896152", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A224", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.226.226", "start_pos": 226, "end_pos": 226, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs727504018", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs727504018", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs727504018", "url": "https://www.ncbi.nlm.nih.gov/snp/rs727504018#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs727504018", "url": "http://gnomad.broadinstitute.org/awesome?query=rs727504018", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs748290939", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748290939", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748290939", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748290939", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748290939", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748290939", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "KKVVVEQLNLLVKRISQQAA", "down_seq": "GNNMEDIFGELLLQLHQQYP", "snv": [ { "evidence": [ { "id": "rs727504018", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs727504018" }, { "id": "rs727504018", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs727504018#frequency_tab" }, { "id": "rs727504018", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs727504018" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896158", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A226", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs748290939", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748290939" }, { "id": "rs748290939", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748290939" }, { "id": "rs748290939", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748290939" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896157", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A226", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs727504018", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs727504018" }, { "id": "rs727504018", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs727504018#frequency_tab" }, { "id": "rs727504018", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs727504018" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896158", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A226", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.227.227", "start_pos": 227, "end_pos": 227, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs747198298", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747198298", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747198298", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747198298", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747198298", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747198298#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs747198298", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747198298", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs747198298", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs747198298", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs557366025", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557366025", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs557366025", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs557366025", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs557366025", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557366025", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs557366025", "url": "https://www.ncbi.nlm.nih.gov/snp/rs557366025#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs557366025", "url": "http://gnomad.broadinstitute.org/awesome?query=rs557366025", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1057517115", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057517115", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "KVVVEQLNLLVKRISQQAAA", "down_seq": "NNMEDIFGELLLQLHQQYPG", "snv": [ { "evidence": [ { "id": "rs747198298", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747198298" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896160", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G227", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs747198298", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747198298" }, { "id": "rs747198298", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747198298" }, { "id": "rs747198298", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747198298#frequency_tab" }, { "id": "rs747198298", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747198298" }, { "id": "rs747198298", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs747198298" }, { "id": "rs557366025", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557366025" }, { "id": "rs557366025", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs557366025" }, { "id": "rs557366025", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557366025" }, { "id": "rs557366025", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs557366025#frequency_tab" }, { "id": "rs557366025", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs557366025" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896160", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G227", "keywords": [ "ebi", "somatic", "germline" ] }, { "evidence": [ { "id": "rs557366025", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557366025" }, { "id": "rs557366025", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs557366025" }, { "id": "rs557366025", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557366025" }, { "id": "rs557366025", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs557366025#frequency_tab" }, { "id": "rs557366025", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs557366025" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896220", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "G227", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1057517115", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057517115" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896221", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G227", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.207.207", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.228.228", "start_pos": 228, "end_pos": 228, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "VVVEQLNLLVKRISQQAAAG", "down_seq": "NMEDIFGELLLQLHQQYPGD", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74896163", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N228", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.208.208", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.22.22", "start_pos": 22, "end_pos": 22, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064709719", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064709719", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064709719", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064709719#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771925493", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771925493", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771925493", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771925493", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771925493", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771925493#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771925493", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771925493", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2505811246", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505811246", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "AAPRVFPLSCAVQQYAWGKM", "down_seq": "SNSEVARLLASSDPLAQIAE", "snv": [ { "evidence": [ { "id": "rs2064709719", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064709719" }, { "id": "rs2064709719", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064709719#frequency_tab" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890575", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G22", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs771925493", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771925493" }, { "id": "rs771925493", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771925493" }, { "id": "rs771925493", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771925493#frequency_tab" }, { "id": "rs771925493", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771925493" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890574", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G22", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505811246", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505811246" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890575", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G22", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.230.230", "start_pos": 230, "end_pos": 230, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs367893149", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs367893149", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs367893149", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs367893149", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs367893149", "url": "https://www.ncbi.nlm.nih.gov/snp/rs367893149#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs367893149", "url": "http://gnomad.broadinstitute.org/awesome?query=rs367893149", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "VEQLNLLVKRISQQAAAGNN", "down_seq": "EDIFGELLLQLHQQYPGDIG", "snv": [ { "evidence": [ { "id": "rs367893149", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs367893149" }, { "id": "rs367893149", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs367893149" }, { "id": "rs367893149", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs367893149#frequency_tab" }, { "id": "rs367893149", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs367893149" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896170", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M230", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs367893149", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs367893149" }, { "id": "rs367893149", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs367893149" }, { "id": "rs367893149", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs367893149#frequency_tab" }, { "id": "rs367893149", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs367893149" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896170", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M230", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.210.210", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.211.211", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs765912695", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765912695", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765912695", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765912695", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765912695", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765912695#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs765912695", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765912695", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1168083953", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1168083953", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1168083953", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1168083953", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs759916229", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759916229", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759916229", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759916229", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759916229", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759916229", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1595822660", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1595822660", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1595822660", "url": "https://www.ensembl.org/id/rs1595822660", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QLNLLVKRISQQAAAGNNME", "down_seq": "IFGELLLQLHQQYPGDIGCF", "snv": [ { "evidence": [ { "id": "rs765912695", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765912695" }, { "id": "rs765912695", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765912695" }, { "id": "rs765912695", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765912695#frequency_tab" }, { "id": "rs765912695", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765912695" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896176", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D232", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1168083953", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1168083953" }, { "id": "rs1168083953", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1168083953" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897012", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D232", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs765912695", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765912695" }, { "id": "rs765912695", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765912695" }, { "id": "rs765912695", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765912695#frequency_tab" }, { "id": "rs765912695", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765912695" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896176", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D232", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs759916229", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759916229" }, { "id": "rs759916229", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759916229" }, { "id": "rs759916229", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759916229" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896175", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D232", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs765912695", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765912695" }, { "id": "rs765912695", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765912695" }, { "id": "rs765912695", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs765912695#frequency_tab" }, { "id": "rs765912695", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765912695" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896176", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D232", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1595822660", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1595822660" }, { "id": "rs1595822660", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1595822660" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896325", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D232", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.233.233", "start_pos": 233, "end_pos": 233, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs776129095", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776129095", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776129095", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776129095", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776129095", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776129095", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "LNLLVKRISQQAAAGNNMED", "down_seq": "FGELLLQLHQQYPGDIGCFA", "snv": [ { "evidence": [ { "id": "rs776129095", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776129095" }, { "id": "rs776129095", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776129095" }, { "id": "rs776129095", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776129095" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896178", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I233", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs776129095", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776129095" }, { "id": "rs776129095", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776129095" }, { "id": "rs776129095", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776129095" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896178", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I233", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.234.234", "start_pos": 234, "end_pos": 234, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1332769798", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1332769798", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1332769798", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1332769798#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1332769798", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1332769798", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "NLLVKRISQQAAAGNNMEDI", "down_seq": "GELLLQLHQQYPGDIGCFAI", "snv": [ { "evidence": [ { "id": "rs1332769798", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1332769798" }, { "id": "rs1332769798", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1332769798#frequency_tab" }, { "id": "rs1332769798", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1332769798" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896182", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F234", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.214.214", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.236.236", "start_pos": 236, "end_pos": 236, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2505825222", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505825222", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "LVKRISQQAAAGNNMEDIFG", "down_seq": "LLLQLHQQYPGDIGCFAIYF", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74896187", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E236", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs2505825222", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505825222" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896187", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E236", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.237.237", "start_pos": 237, "end_pos": 237, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs767145258", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767145258", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767145258", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767145258", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767145258", "url": "https://www.ncbi.nlm.nih.gov/snp/rs767145258#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs767145258", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767145258", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2064816624", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064816624", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064816624", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064816624#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "VKRISQQAAAGNNMEDIFGE", "down_seq": "LLQLHQQYPGDIGCFAIYFL", "snv": [ { "evidence": [ { "id": "rs767145258", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767145258" }, { "id": "rs767145258", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767145258" }, { "id": "rs767145258", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs767145258#frequency_tab" }, { "id": "rs767145258", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767145258" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896190", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L237", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2064816624", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064816624" }, { "id": "rs2064816624", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064816624#frequency_tab" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896251", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L237", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs767145258", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767145258" }, { "id": "rs767145258", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767145258" }, { "id": "rs767145258", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs767145258#frequency_tab" }, { "id": "rs767145258", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767145258" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896190", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L237", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.217.217", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.238.238", "start_pos": 238, "end_pos": 238, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2505825283", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505825283", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs745432667", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745432667", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "KRISQQAAAGNNMEDIFGEL", "down_seq": "LQLHQQYPGDIGCFAIYFLN", "snv": [ { "evidence": [ { "id": "rs2505825283", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505825283" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896194", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L238", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs745432667", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745432667" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896194", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L238", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.218.218", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.23.23", "start_pos": 23, "end_pos": 23, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1452964686", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1452964686", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1452964686", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1452964686", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "APRVFPLSCAVQQYAWGKMG", "down_seq": "NSEVARLLASSDPLAQIAED", "snv": [ { "evidence": [ { "id": "rs1452964686", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1452964686" }, { "id": "rs1452964686", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1452964686" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890578", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S23", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.240.240", "start_pos": 240, "end_pos": 240, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs776340315", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776340315", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776340315", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776340315#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs776340315", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776340315", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "ISQQAAAGNNMEDIFGELLL", "down_seq": "LHQQYPGDIGCFAIYFLNLL", "snv": [ { "evidence": [ { "id": "rs776340315", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776340315" }, { "id": "rs776340315", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776340315#frequency_tab" }, { "id": "rs776340315", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776340315" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896199", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q240", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.220.220", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.241.241", "start_pos": 241, "end_pos": 241, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "SQQAAAGNNMEDIFGELLLQ", "down_seq": "HQQYPGDIGCFAIYFLNLLT", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74896202", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "L241", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.221.221", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.243.243", "start_pos": 243, "end_pos": 243, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs749911553", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749911553", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs749911553", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749911553", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs749911553", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749911553", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2064815550", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064815550", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064815550", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064815550#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "QAAAGNNMEDIFGELLLQLH", "down_seq": "QYPGDIGCFAIYFLNLLTLK", "snv": [ { "evidence": [ { "id": "rs749911553", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749911553" }, { "id": "rs749911553", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749911553" }, { "id": "rs749911553", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749911553" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896208", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q243", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs2064815550", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064815550" }, { "id": "rs2064815550", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064815550#frequency_tab" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896210", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q243", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.224.224", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.246.246", "start_pos": 246, "end_pos": 246, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1373231619", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1373231619", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1373231619", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1373231619", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "AGNNMEDIFGELLLQLHQQY", "down_seq": "GDIGCFAIYFLNLLTLKPGE", "snv": [ { "evidence": [ { "id": "rs1373231619", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1373231619" }, { "id": "rs1373231619", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1373231619" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896218", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P246", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.247.247", "start_pos": 247, "end_pos": 247, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs557366025", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557366025", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs557366025", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs557366025", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs557366025", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557366025", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs557366025", "url": "https://www.ncbi.nlm.nih.gov/snp/rs557366025#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs557366025", "url": "http://gnomad.broadinstitute.org/awesome?query=rs557366025", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1220130042", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1220130042", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1220130042", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1220130042", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1057517115", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057517115", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GNNMEDIFGELLLQLHQQYP", "down_seq": "DIGCFAIYFLNLLTLKPGEA", "snv": [ { "evidence": [ { "id": "rs557366025", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557366025" }, { "id": "rs557366025", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs557366025" }, { "id": "rs557366025", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557366025" }, { "id": "rs557366025", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs557366025#frequency_tab" }, { "id": "rs557366025", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs557366025" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896220", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "G247", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs557366025", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557366025" }, { "id": "rs557366025", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs557366025" }, { "id": "rs557366025", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557366025" }, { "id": "rs557366025", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs557366025#frequency_tab" }, { "id": "rs557366025", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs557366025" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896220", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "G247", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1220130042", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1220130042" }, { "id": "rs1220130042", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1220130042" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897056", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G247", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1057517115", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057517115" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896221", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G247", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.227.227", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.228.228", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.249.249", "start_pos": 249, "end_pos": 249, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201676072", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201676072", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201676072", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201676072", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201676072", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201676072", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201676072", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201676072", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2064815841", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064815841", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064815841", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064815841#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2064815841", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064815841", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2141206676", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141206676", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "NMEDIFGELLLQLHQQYPGD", "down_seq": "GCFAIYFLNLLTLKPGEAMF", "snv": [ { "evidence": [ { "id": "rs201676072", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201676072" }, { "id": "rs201676072", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201676072" }, { "id": "rs201676072", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201676072" }, { "id": "rs201676072", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201676072" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896227", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "I249", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs201676072", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201676072" }, { "id": "rs201676072", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201676072" }, { "id": "rs201676072", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201676072" }, { "id": "rs201676072", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201676072" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896227", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "I249", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs201676072", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201676072" }, { "id": "rs201676072", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201676072" }, { "id": "rs201676072", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201676072" }, { "id": "rs201676072", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201676072" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896227", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "I249", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs2064815841", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064815841" }, { "id": "rs2064815841", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064815841#frequency_tab" }, { "id": "rs2064815841", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064815841" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896226", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I249", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2141206676", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141206676" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896226", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I249", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.24.24", "start_pos": 24, "end_pos": 24, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs746378460", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746378460", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746378460", "url": "https://www.ensembl.org/id/rs746378460", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "PRVFPLSCAVQQYAWGKMGS", "down_seq": "SEVARLLASSDPLAQIAEDK", "snv": [ { "evidence": [ { "id": "rs746378460", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746378460" }, { "id": "rs746378460", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs746378460" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890581", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N24", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.250.250", "start_pos": 250, "end_pos": 250, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2074183138", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2074183138", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2074183138", "url": "https://www.ensembl.org/id/rs2074183138", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs748090636", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748090636", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748090636", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748090636", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748090636", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748090636#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs748090636", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748090636", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "MEDIFGELLLQLHQQYPGDI", "down_seq": "CFAIYFLNLLTLKPGEAMFL", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs2074183138", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2074183138" }, { "id": "rs2074183138", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2074183138" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74896230", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G250", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs748090636", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748090636" }, { "id": "rs748090636", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748090636" }, { "id": "rs748090636", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748090636#frequency_tab" }, { "id": "rs748090636", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748090636" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896229", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G250", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs748090636", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748090636" }, { "id": "rs748090636", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748090636" }, { "id": "rs748090636", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748090636#frequency_tab" }, { "id": "rs748090636", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748090636" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896229", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G250", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.251.251", "start_pos": 251, "end_pos": 251, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1194425483", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194425483", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1194425483", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194425483", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs191159836", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs191159836", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs191159836", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs191159836", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs191159836", "url": "http://gnomad.broadinstitute.org/awesome?query=rs191159836", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs191159836", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs191159836", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs2505825473", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505825473", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "EDIFGELLLQLHQQYPGDIG", "down_seq": "FAIYFLNLLTLKPGEAMFLE", "snv": [ { "evidence": [ { "id": "rs1194425483", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194425483" }, { "id": "rs1194425483", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194425483" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896232", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C251", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs191159836", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs191159836" }, { "id": "rs191159836", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs191159836" }, { "id": "rs191159836", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs191159836" }, { "id": "rs191159836", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs191159836" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "C", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74896234", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "C251", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "C", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74896233", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "C251", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs2505825473", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505825473" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896232", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C251", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.252.252", "start_pos": 252, "end_pos": 252, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1170222903", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1170222903", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1170222903", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1170222903", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs543652740", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs543652740", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs543652740", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs543652740", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs543652740", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs543652740", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs543652740", "url": "https://www.ncbi.nlm.nih.gov/snp/rs543652740#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs543652740", "url": "http://gnomad.broadinstitute.org/awesome?query=rs543652740", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2141206722", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141206722", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "DIFGELLLQLHQQYPGDIGC", "down_seq": "AIYFLNLLTLKPGEAMFLEA", "snv": [ { "evidence": [ { "id": "rs1170222903", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1170222903" }, { "id": "rs1170222903", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1170222903" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896236", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F252", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs543652740", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs543652740" }, { "id": "rs543652740", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs543652740" }, { "id": "rs543652740", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs543652740" }, { "id": "rs543652740", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs543652740#frequency_tab" }, { "id": "rs543652740", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs543652740" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896235", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "F252", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs543652740", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs543652740" }, { "id": "rs543652740", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs543652740" }, { "id": "rs543652740", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs543652740" }, { "id": "rs543652740", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs543652740#frequency_tab" }, { "id": "rs543652740", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs543652740" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896235", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "F252", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2141206722", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141206722" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896234", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F252", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.253.253", "start_pos": 253, "end_pos": 253, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs771100056", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771100056", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771100056", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771100056", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771100056", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771100056", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs771100056", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs771100056", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "IFGELLLQLHQQYPGDIGCF", "down_seq": "IYFLNLLTLKPGEAMFLEAN", "snv": [ { "evidence": [ { "id": "rs771100056", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771100056" }, { "id": "rs771100056", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771100056" }, { "id": "rs771100056", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771100056" }, { "id": "rs771100056", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs771100056" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896239", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A253", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.233.233", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.234.234", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.255.255", "start_pos": 255, "end_pos": 255, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs746276252", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746276252", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746276252", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746276252", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs746276252", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746276252", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2505825556", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505825556", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2505825546", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505825546", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "GELLLQLHQQYPGDIGCFAI", "down_seq": "FLNLLTLKPGEAMFLEANVP", "snv": [ { "evidence": [ { "id": "rs746276252", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746276252" }, { "id": "rs746276252", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746276252" }, { "id": "rs746276252", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746276252" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896246", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y255", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505825556", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505825556" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896245", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y255", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs2505825546", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505825546" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896245_74896257", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y255", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.256.256", "start_pos": 256, "end_pos": 256, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1442151213", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1442151213", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1442151213", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1442151213#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1442151213", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1442151213", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "ELLLQLHQQYPGDIGCFAIY", "down_seq": "LNLLTLKPGEAMFLEANVPH", "snv": [ { "evidence": [ { "id": "rs1442151213", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1442151213" }, { "id": "rs1442151213", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1442151213#frequency_tab" }, { "id": "rs1442151213", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1442151213" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896248", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F256", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.236.236", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.257.257", "start_pos": 257, "end_pos": 257, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064816624", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064816624", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064816624", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064816624#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "LLLQLHQQYPGDIGCFAIYF", "down_seq": "NLLTLKPGEAMFLEANVPHA", "snv": [ { "evidence": [ { "id": "rs2064816624", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064816624" }, { "id": "rs2064816624", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064816624#frequency_tab" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896251", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L257", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.237.237", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.258.258", "start_pos": 258, "end_pos": 258, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LLQLHQQYPGDIGCFAIYFL", "down_seq": "LLTLKPGEAMFLEANVPHAY", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74896254", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N258", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.238.238", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.260.260", "start_pos": 260, "end_pos": 260, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1299431062", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1299431062", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1299431062", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1299431062", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1299431062", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1299431062", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "QLHQQYPGDIGCFAIYFLNL", "down_seq": "TLKPGEAMFLEANVPHAYLK", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs1299431062", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1299431062" }, { "id": "rs1299431062", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1299431062" }, { "id": "rs1299431062", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1299431062" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74896259", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "L260", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.240.240", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.261.261", "start_pos": 261, "end_pos": 261, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064816825", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064816825", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064816825", "url": "https://www.ensembl.org/id/rs2064816825", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LHQQYPGDIGCFAIYFLNLL", "down_seq": "LKPGEAMFLEANVPHAYLKG", "snv": [ { "evidence": [ { "id": "rs2064816825", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064816825" }, { "id": "rs2064816825", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064816825" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896262", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T261", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.241.241", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.262.262", "start_pos": 262, "end_pos": 262, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1356646703", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1356646703", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1356646703", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1356646703#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1356646703", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1356646703", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1398918834", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1398918834", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1398918834", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1398918834", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "HQQYPGDIGCFAIYFLNLLT", "down_seq": "KPGEAMFLEANVPHAYLKGD", "snv": [ { "evidence": [ { "id": "rs1356646703", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1356646703" }, { "id": "rs1356646703", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1356646703#frequency_tab" }, { "id": "rs1356646703", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1356646703" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897100", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L262", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1398918834", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1398918834" }, { "id": "rs1398918834", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1398918834" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896266", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L262", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.263.263", "start_pos": 263, "end_pos": 263, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064816963", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064816963", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064816963", "url": "https://www.ensembl.org/id/rs2064816963", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "QQYPGDIGCFAIYFLNLLTL", "down_seq": "PGEAMFLEANVPHAYLKGDC", "snv": [ { "evidence": [ { "id": "rs2064816963", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064816963" }, { "id": "rs2064816963", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064816963" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896270", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K263", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.243.243", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.264.264", "start_pos": 264, "end_pos": 264, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs141650977", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141650977", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs141650977", "url": "https://www.ncbi.nlm.nih.gov/snp/rs141650977#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2064818123", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064818123", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064818123", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064818123#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2064818123", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064818123", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "QYPGDIGCFAIYFLNLLTLK", "down_seq": "GEAMFLEANVPHAYLKGDCV", "snv": [ { "evidence": [ { "id": "rs141650977", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141650977" }, { "id": "rs141650977", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs141650977#frequency_tab" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896272", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P264", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs141650977", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141650977" }, { "id": "rs141650977", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs141650977#frequency_tab" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896272", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P264", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs2064818123", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064818123" }, { "id": "rs2064818123", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064818123#frequency_tab" }, { "id": "rs2064818123", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064818123" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74896271", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P264", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.265.265", "start_pos": 265, "end_pos": 265, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1230728792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1230728792", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1230728792", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1230728792#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1230728792", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1230728792", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2064817105", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064817105", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064817105", "url": "https://www.ensembl.org/id/rs2064817105", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1313637977", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1313637977", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "YPGDIGCFAIYFLNLLTLKP", "down_seq": "EAMFLEANVPHAYLKGDCVE", "snv": [ { "evidence": [ { "id": "rs1230728792", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1230728792" }, { "id": "rs1230728792", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1230728792#frequency_tab" }, { "id": "rs1230728792", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1230728792" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896275", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G265", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2064817105", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064817105" }, { "id": "rs2064817105", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064817105" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896274", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G265", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "G", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74896275", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G265", "disease": [ { "disease_id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." }, "synonyms": [ { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "tumor of the Ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "A primary or metastatic malignant neoplasm involving the ovary. Most primary malignant ovarian neoplasms are either carcinomas (serous, mucinous, or endometrioid adenocarcinomas) or malignant germ cell tumors. Metastatic malignant neoplasms to the ovary include carcinomas, lymphomas, and melanomas." }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74896274", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G265", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1313637977", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1313637977" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896273", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G265", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.266.266", "start_pos": 266, "end_pos": 266, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1595822583", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1595822583", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1595822583", "url": "https://www.ensembl.org/id/rs1595822583", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "PGDIGCFAIYFLNLLTLKPG", "down_seq": "AMFLEANVPHAYLKGDCVEC", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs1595822583", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1595822583" }, { "id": "rs1595822583", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1595822583" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74896277", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E266", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.246.246", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.247.247", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.268.268", "start_pos": 268, "end_pos": 268, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1169592252", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1169592252", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1169592252", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1169592252#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs763589568", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763589568", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763589568", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763589568", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763589568", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763589568", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1555479227", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555479227", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "DIGCFAIYFLNLLTLKPGEA", "down_seq": "FLEANVPHAYLKGDCVECMA", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs1169592252", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1169592252" }, { "id": "rs1169592252", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1169592252#frequency_tab" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "M", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74896284", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "M268", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs763589568", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763589568" }, { "id": "rs763589568", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763589568" }, { "id": "rs763589568", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763589568" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896283", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M268", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1555479227", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555479227" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896283_74896284", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M268", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.249.249", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.26.26", "start_pos": 26, "end_pos": 26, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760694473", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760694473", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760694473", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760694473", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760694473", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760694473#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs760694473", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760694473", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs760694473", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs760694473", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1596440826", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1596440826", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1596440826", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1596440826#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "VFPLSCAVQQYAWGKMGSNS", "down_seq": "VARLLASSDPLAQIAEDKPY", "snv": [ { "evidence": [ { "id": "rs760694473", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760694473" }, { "id": "rs760694473", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760694473" }, { "id": "rs760694473", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760694473#frequency_tab" }, { "id": "rs760694473", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760694473" }, { "id": "rs760694473", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs760694473" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890586", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E26", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1596440826", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1596440826" }, { "id": "rs1596440826", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1596440826#frequency_tab" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890588", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E26", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760694473", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760694473" }, { "id": "rs760694473", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760694473" }, { "id": "rs760694473", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760694473#frequency_tab" }, { "id": "rs760694473", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760694473" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890586", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E26", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.270.270", "start_pos": 270, "end_pos": 270, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs979231891", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs979231891", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs979231891", "url": "https://www.ncbi.nlm.nih.gov/snp/rs979231891#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs979231891", "url": "http://gnomad.broadinstitute.org/awesome?query=rs979231891", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "GCFAIYFLNLLTLKPGEAMF", "down_seq": "EANVPHAYLKGDCVECMACS", "snv": [ { "evidence": [ { "id": "rs979231891", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs979231891" }, { "id": "rs979231891", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs979231891#frequency_tab" }, { "id": "rs979231891", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs979231891" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896290", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L270", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.250.250", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.271.271", "start_pos": 271, "end_pos": 271, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064817409", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064817409", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064817409", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064817409", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "CFAIYFLNLLTLKPGEAMFL", "down_seq": "ANVPHAYLKGDCVECMACSD", "snv": [ { "evidence": [ { "id": "rs2064817409", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064817409" }, { "id": "rs2064817409", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064817409" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896292", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E271", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.251.251", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.272.272", "start_pos": 272, "end_pos": 272, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs769238714", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769238714", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769238714", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769238714", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769238714", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769238714", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "FAIYFLNLLTLKPGEAMFLE", "down_seq": "NVPHAYLKGDCVECMACSDN", "snv": [ { "evidence": [ { "id": "rs769238714", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769238714" }, { "id": "rs769238714", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769238714" }, { "id": "rs769238714", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769238714" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896296", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A272", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.252.252", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.273.273", "start_pos": 273, "end_pos": 273, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs576592379", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs576592379", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs576592379", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs576592379", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs576592379", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs576592379", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs576592379", "url": "https://www.ncbi.nlm.nih.gov/snp/rs576592379#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs576592379", "url": "http://gnomad.broadinstitute.org/awesome?query=rs576592379", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs150525282", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150525282", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs150525282", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150525282", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs150525282", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150525282", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs150525282", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150525282#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs150525282", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150525282", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2505825772", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505825772", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "AIYFLNLLTLKPGEAMFLEA", "down_seq": "VPHAYLKGDCVECMACSDNT", "snv": [ { "evidence": [ { "id": "rs576592379", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs576592379" }, { "id": "rs576592379", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs576592379" }, { "id": "rs576592379", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs576592379" }, { "id": "rs576592379", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs576592379#frequency_tab" }, { "id": "rs576592379", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs576592379" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896300", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "N273", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs150525282", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150525282" }, { "id": "rs150525282", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150525282" }, { "id": "rs150525282", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150525282" }, { "id": "rs150525282", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150525282#frequency_tab" }, { "id": "rs150525282", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150525282" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896299", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0", "site_lbl": "N273", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ] }, { "evidence": [ { "id": "rs2505825772", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505825772" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896299delin", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N273", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.253.253", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.275.275", "start_pos": 275, "end_pos": 275, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs540858898", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs540858898", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs540858898", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs540858898", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs540858898", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs540858898", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs540858898", "url": "https://www.ncbi.nlm.nih.gov/snp/rs540858898#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs540858898", "url": "http://gnomad.broadinstitute.org/awesome?query=rs540858898", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "YFLNLLTLKPGEAMFLEANV", "down_seq": "HAYLKGDCVECMACSDNTVR", "snv": [ { "evidence": [ { "id": "rs540858898", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs540858898" }, { "id": "rs540858898", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs540858898" }, { "id": "rs540858898", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs540858898" }, { "id": "rs540858898", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs540858898#frequency_tab" }, { "id": "rs540858898", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs540858898" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896304", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "P275", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.255.255", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.256.256", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.277.277", "start_pos": 277, "end_pos": 277, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064818530", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064818530", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064818530", "url": "https://www.ensembl.org/id/rs2064818530", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs759130781", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759130781", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759130781", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759130781", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759130781", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759130781#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs759130781", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759130781", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs781076595", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781076595", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781076595", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781076595", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781076595", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781076595#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs781076595", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781076595", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1567268682", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567268682", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LNLLTLKPGEAMFLEANVPH", "down_seq": "YLKGDCVECMACSDNTVRAG", "snv": [ { "evidence": [ { "id": "rs2064818530", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064818530" }, { "id": "rs2064818530", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064818530" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896371", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A277", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs759130781", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759130781" }, { "id": "rs759130781", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759130781" }, { "id": "rs759130781", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759130781#frequency_tab" }, { "id": "rs759130781", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759130781" }, { "id": "rs781076595", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781076595" }, { "id": "rs781076595", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781076595" }, { "id": "rs781076595", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781076595#frequency_tab" }, { "id": "rs781076595", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781076595" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896310", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A277", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1567268682", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567268682" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896311_74896312", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A277", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.257.257", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.278.278", "start_pos": 278, "end_pos": 278, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200808502", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200808502", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200808502", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200808502", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs200808502", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200808502", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200808502", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200808502#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "NLLTLKPGEAMFLEANVPHA", "down_seq": "LKGDCVECMACSDNTVRAGL", "snv": [ { "evidence": [ { "id": "rs200808502", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200808502" }, { "id": "rs200808502", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200808502" }, { "id": "rs200808502", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200808502" }, { "id": "rs200808502", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200808502#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896314", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y278", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.258.258", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.260.260", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.27.27", "start_pos": 27, "end_pos": 27, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs368328510", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368328510", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs368328510", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368328510#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "FPLSCAVQQYAWGKMGSNSE", "down_seq": "ARLLASSDPLAQIAEDKPYA", "snv": [ { "evidence": [ { "id": "rs368328510", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs368328510" }, { "id": "rs368328510", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs368328510#frequency_tab" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890589", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V27", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.281.281", "start_pos": 281, "end_pos": 281, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752447493", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752447493", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752447493", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752447493", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752447493", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752447493", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs758352713", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758352713", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758352713", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758352713", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758352713", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758352713#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs758352713", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758352713", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "TLKPGEAMFLEANVPHAYLK", "down_seq": "DCVECMACSDNTVRAGLTPK", "snv": [ { "evidence": [ { "id": "rs752447493", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752447493" }, { "id": "rs752447493", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752447493" }, { "id": "rs752447493", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752447493" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896322", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G281", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs758352713", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758352713" }, { "id": "rs758352713", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758352713" }, { "id": "rs758352713", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758352713#frequency_tab" }, { "id": "rs758352713", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758352713" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896323", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G281", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.261.261", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.282.282", "start_pos": 282, "end_pos": 282, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1168083953", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1168083953", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1168083953", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1168083953", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2505829354", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505829354", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1595822660", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1595822660", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1595822660", "url": "https://www.ensembl.org/id/rs1595822660", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LKPGEAMFLEANVPHAYLKG", "down_seq": "CVECMACSDNTVRAGLTPKF", "snv": [ { "evidence": [ { "id": "rs1168083953", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1168083953" }, { "id": "rs1168083953", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1168083953" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897012", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D282", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505829354", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505829354" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897161", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D282", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1595822660", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1595822660" }, { "id": "rs1595822660", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1595822660" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896325", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D282", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.262.262", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.283.283", "start_pos": 283, "end_pos": 283, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1418395401", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1418395401", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1418395401", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1418395401", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "KPGEAMFLEANVPHAYLKGD", "down_seq": "VECMACSDNTVRAGLTPKFI", "snv": [ { "evidence": [ { "id": "rs1418395401", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1418395401" }, { "id": "rs1418395401", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1418395401" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897014", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C283", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.263.263", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.284.284", "start_pos": 284, "end_pos": 284, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs745358856", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745358856", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs745358856", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745358856", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs745358856", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745358856#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs745358856", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745358856", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "PGEAMFLEANVPHAYLKGDC", "down_seq": "ECMACSDNTVRAGLTPKFID", "snv": [ { "evidence": [ { "id": "rs745358856", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745358856" }, { "id": "rs745358856", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745358856" }, { "id": "rs745358856", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745358856#frequency_tab" }, { "id": "rs745358856", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745358856" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897016", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V284", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.264.264", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.265.265", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.286.286", "start_pos": 286, "end_pos": 286, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1413178554", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1413178554", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1413178554", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1413178554#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1413178554", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1413178554", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs764476271", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764476271", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764476271", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764476271", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764476271", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764476271", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1274593112", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1274593112", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1274593112", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1274593112", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2064839839", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064839839", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "EAMFLEANVPHAYLKGDCVE", "down_seq": "MACSDNTVRAGLTPKFIDVP", "snv": [ { "evidence": [ { "id": "rs1413178554", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1413178554" }, { "id": "rs1413178554", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1413178554#frequency_tab" }, { "id": "rs1413178554", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1413178554" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897022", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C286", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs764476271", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764476271" }, { "id": "rs764476271", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764476271" }, { "id": "rs764476271", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764476271" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897524", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C286", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs764476271", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764476271" }, { "id": "rs764476271", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764476271" }, { "id": "rs764476271", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764476271" }, { "id": "rs1274593112", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1274593112" }, { "id": "rs1274593112", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1274593112" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897524", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C286", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2064839839", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064839839" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897520CT", "ref_nt": "]", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C286", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.266.266", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.288.288", "start_pos": 288, "end_pos": 288, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1159367765", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1159367765", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1159367765", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1159367765#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs775111649", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775111649", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775111649", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775111649", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775111649", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775111649#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs775111649", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775111649", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs775111649", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs775111649", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "MFLEANVPHAYLKGDCVECM", "down_seq": "CSDNTVRAGLTPKFIDVPTL", "snv": [ { "evidence": [ { "id": "rs1159367765", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1159367765" }, { "id": "rs1159367765", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1159367765#frequency_tab" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897028", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A288", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs775111649", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775111649" }, { "id": "rs775111649", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775111649" }, { "id": "rs775111649", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775111649#frequency_tab" }, { "id": "rs775111649", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775111649" }, { "id": "rs775111649", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs775111649" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897029", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A288", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.268.268", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.289.289", "start_pos": 289, "end_pos": 289, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1433931750", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1433931750", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1433931750", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1433931750", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "FLEANVPHAYLKGDCVECMA", "down_seq": "SDNTVRAGLTPKFIDVPTLC", "snv": [ { "evidence": [ { "id": "rs1433931750", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1433931750" }, { "id": "rs1433931750", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1433931750" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897092", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C289", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PLSCAVQQYAWGKMGSNSEV", "down_seq": "RLLASSDPLAQIAEDKPYAE", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74890593", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A28", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.290.290", "start_pos": 290, "end_pos": 290, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1469654026", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1469654026", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1469654026", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1469654026#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1469654026", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1469654026", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LEANVPHAYLKGDCVECMAC", "down_seq": "DNTVRAGLTPKFIDVPTLCE", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs1469654026", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1469654026" }, { "id": "rs1469654026", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1469654026#frequency_tab" }, { "id": "rs1469654026", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1469654026" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "719", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897035", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S290", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.270.270", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.291.291", "start_pos": 291, "end_pos": 291, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1312289762", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1312289762", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1312289762", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1312289762", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "EANVPHAYLKGDCVECMACS", "down_seq": "NTVRAGLTPKFIDVPTLCEM", "snv": [ { "evidence": [ { "id": "rs1312289762", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1312289762" }, { "id": "rs1312289762", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1312289762" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897037", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D291", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1312289762", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1312289762" }, { "id": "rs1312289762", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1312289762" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897037", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D291", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.272.272", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.293.293", "start_pos": 293, "end_pos": 293, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1400630017", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1400630017", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1400630017", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1400630017", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs775936635", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775936635", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775936635", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775936635", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775936635", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775936635#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs775936635", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775936635", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NVPHAYLKGDCVECMACSDN", "down_seq": "VRAGLTPKFIDVPTLCEMLS", "snv": [ { "evidence": [ { "id": "rs1400630017", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1400630017" }, { "id": "rs1400630017", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1400630017" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896418", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T293", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs775936635", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775936635" }, { "id": "rs775936635", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775936635" }, { "id": "rs775936635", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775936635#frequency_tab" }, { "id": "rs775936635", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775936635" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896419", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T293", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs775936635", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775936635" }, { "id": "rs775936635", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775936635" }, { "id": "rs775936635", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775936635#frequency_tab" }, { "id": "rs775936635", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775936635" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896419", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T293", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.273.273", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.294.294", "start_pos": 294, "end_pos": 294, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2505828744", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505828744", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1555479351", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555479351", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "VPHAYLKGDCVECMACSDNT", "down_seq": "RAGLTPKFIDVPTLCEMLSY", "snv": [ { "evidence": [ { "id": "rs2505828744", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505828744" }, { "id": "rs1555479351", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555479351" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897041_74897045", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V294", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.295.295", "start_pos": 295, "end_pos": 295, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Protein losing enteropathy-hepatic fibrosis syndrome in Saguenay-Lac St-Jean, Quebec is a congenital disorder of glycosylation type Ib.", "journal": "Journal of medical genetics", "date": "2002", "authors": "Vuillaumier-Barrot S, Le Bizec C, de Lonlay P, Barnier A, Mitchell G, Pelletier V, Prevost C, Saudubray JM, Durand G, Seta N", "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" }, { "database": "Reactome", "id": "R-HSA-4043916", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-4043916" }, { "database": "dbSNP", "id": "rs28928906", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs28928906" } ], "reference": [ { "type": "PubMed", "id": "12414827", "url": "https://glygen.org/publication/PubMed/12414827" } ] }, { "title": "Secretory diarrhea with protein-losing enteropathy, enterocolitis cystica superficialis, intestinal lymphangiectasia, and congenital hepatic fibrosis: a new syndrome.", "journal": "The Journal of pediatrics", "date": "1986", "authors": "Pelletier VA, Galeano N, Brochu P, Morin CL, Weber AM, Roy CC", "evidence": [ { "database": "Reactome", "id": "R-HSA-4043916", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-4043916" }, { "database": "dbSNP", "id": "rs28928906", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs28928906" } ], "reference": [ { "type": "PubMed", "id": "3080572", "url": "https://glygen.org/publication/PubMed/3080572" } ] } ], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs374817183", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374817183", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs374817183", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374817183", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs374817183", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374817183#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs374817183", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374817183", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs374817183", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs374817183", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs28928906", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs28928906", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs28928906", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs28928906", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs28928906", "url": "https://www.ncbi.nlm.nih.gov/snp/rs28928906#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs28928906", "url": "http://gnomad.broadinstitute.org/awesome?query=rs28928906", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "12414827", "url": "https://glygen.org/publication/PubMed/12414827", "database": "PubMed", "categories": [ "Other" ] }, { "id": "3080572", "url": "https://glygen.org/publication/PubMed/3080572", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PHAYLKGDCVECMACSDNTV", "down_seq": "AGLTPKFIDVPTLCEMLSYT", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs374817183", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374817183" }, { "id": "rs374817183", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374817183" }, { "id": "rs374817183", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374817183#frequency_tab" }, { "id": "rs374817183", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374817183" }, { "id": "rs374817183", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs374817183" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897049", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R295", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs28928906", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs28928906" }, { "id": "rs28928906", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs28928906" }, { "id": "rs28928906", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs28928906#frequency_tab" }, { "id": "rs28928906", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs28928906" }, { "id": "12414827", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/12414827" }, { "id": "3080572", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/3080572" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897050", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R295", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.275.275", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P34949-1.297.297", "start_pos": 297, "end_pos": 297, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1220130042", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1220130042", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1220130042", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1220130042", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "AYLKGDCVECMACSDNTVRA", "down_seq": "LTPKFIDVPTLCEMLSYTPS", "snv": [ { "evidence": [ { "id": "rs1220130042", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1220130042" }, { "id": "rs1220130042", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1220130042" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897056", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G297", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.277.277", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.298.298", "start_pos": 298, "end_pos": 298, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1254527884", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1254527884", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1254527884", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1254527884", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs773981017", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773981017", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773981017", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773981017", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773981017", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773981017", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1377346641", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1377346641", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1377346641", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1377346641", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "YLKGDCVECMACSDNTVRAG", "down_seq": "TPKFIDVPTLCEMLSYTPSS", "snv": [ { "evidence": [ { "id": "rs1254527884", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1254527884" }, { "id": "rs1254527884", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1254527884" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896374", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L298", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs773981017", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773981017" }, { "id": "rs773981017", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773981017" }, { "id": "rs773981017", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773981017" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897059", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L298", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1377346641", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1377346641" }, { "id": "rs1377346641", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1377346641" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896373", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L298", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.278.278", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.299.299", "start_pos": 299, "end_pos": 299, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2141208417", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141208417", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2141208417", "url": "https://www.ensembl.org/id/rs2141208417", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs761837484", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761837484", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs761837484", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761837484", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs761837484", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761837484", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LKGDCVECMACSDNTVRAGL", "down_seq": "PKFIDVPTLCEMLSYTPSSS", "snv": [ { "evidence": [ { "id": "rs2141208417", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141208417" }, { "id": "rs2141208417", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2141208417" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897061", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T299", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs761837484", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761837484" }, { "id": "rs761837484", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761837484" }, { "id": "rs761837484", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761837484" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897062", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T299", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.29.29", "start_pos": 29, "end_pos": 29, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs776716451", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776716451", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776716451", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776716451", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776716451", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776716451", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs771189485", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771189485", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771189485", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771189485", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771189485", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771189485", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs753839890", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753839890", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LSCAVQQYAWGKMGSNSEVA", "down_seq": "LLASSDPLAQIAEDKPYAEL", "snv": [ { "evidence": [ { "id": "rs776716451", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776716451" }, { "id": "rs776716451", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776716451" }, { "id": "rs776716451", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776716451" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890596", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R29", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs771189485", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771189485" }, { "id": "rs771189485", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771189485" }, { "id": "rs771189485", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771189485" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890595", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R29", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs753839890", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753839890" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890594_74890598", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R29", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.2.2", "start_pos": 2, "end_pos": 2, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1254866437", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1254866437", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1254866437", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1254866437#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1254866437", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1254866437", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "M", "down_seq": "APRVFPLSCAVQQYAWGKMG", "snv": [ { "evidence": [ { "id": "rs1254866437", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1254866437" }, { "id": "rs1254866437", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1254866437#frequency_tab" }, { "id": "rs1254866437", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1254866437" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890078", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A2", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P34949-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.300.300", "start_pos": 300, "end_pos": 300, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs746095932", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746095932", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746095932", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746095932", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs746095932", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746095932#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs746095932", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746095932", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs750574993", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750574993", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750574993", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750574993", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750574993", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750574993", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs767336792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767336792", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767336792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767336792", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767336792", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767336792", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "KGDCVECMACSDNTVRAGLT", "down_seq": "KFIDVPTLCEMLSYTPSSSK", "snv": [ { "evidence": [ { "id": "rs746095932", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746095932" }, { "id": "rs746095932", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746095932" }, { "id": "rs746095932", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746095932#frequency_tab" }, { "id": "rs746095932", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746095932" }, { "id": "rs750574993", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750574993" }, { "id": "rs750574993", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750574993" }, { "id": "rs750574993", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750574993" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74896380", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P300", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs767336792", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767336792" }, { "id": "rs767336792", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767336792" }, { "id": "rs767336792", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767336792" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897064", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P300", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.301.301", "start_pos": 301, "end_pos": 301, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs534508637", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534508637", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs534508637", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs534508637", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs534508637", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534508637", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs534508637", "url": "https://www.ncbi.nlm.nih.gov/snp/rs534508637#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs534508637", "url": "http://gnomad.broadinstitute.org/awesome?query=rs534508637", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "GDCVECMACSDNTVRAGLTP", "down_seq": "FIDVPTLCEMLSYTPSSSKD", "snv": [ { "evidence": [ { "id": "rs534508637", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534508637" }, { "id": "rs534508637", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs534508637" }, { "id": "rs534508637", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534508637" }, { "id": "rs534508637", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs534508637#frequency_tab" }, { "id": "rs534508637", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs534508637" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897068", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "K301", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs534508637", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534508637" }, { "id": "rs534508637", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs534508637" }, { "id": "rs534508637", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534508637" }, { "id": "rs534508637", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs534508637#frequency_tab" }, { "id": "rs534508637", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs534508637" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897068", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "K301", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.281.281", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.282.282", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.303.303", "start_pos": 303, "end_pos": 303, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1241106775", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1241106775", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1241106775", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1241106775", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs139866632", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139866632", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs139866632", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs139866632", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs139866632", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139866632", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs139866632", "url": "https://www.ncbi.nlm.nih.gov/snp/rs139866632#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs139866632", "url": "http://gnomad.broadinstitute.org/awesome?query=rs139866632", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "CVECMACSDNTVRAGLTPKF", "down_seq": "DVPTLCEMLSYTPSSSKDRL", "snv": [ { "evidence": [ { "id": "rs1241106775", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1241106775" }, { "id": "rs1241106775", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1241106775" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897075", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I303", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs139866632", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139866632" }, { "id": "rs139866632", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs139866632" }, { "id": "rs139866632", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs139866632" }, { "id": "rs139866632", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs139866632#frequency_tab" }, { "id": "rs139866632", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs139866632" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897074", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "I303", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.283.283", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.304.304", "start_pos": 304, "end_pos": 304, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs754124034", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754124034", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs754124034", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754124034", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs754124034", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754124034", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2064829355", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064829355", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064829355", "url": "https://www.ensembl.org/id/rs2064829355", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VECMACSDNTVRAGLTPKFI", "down_seq": "VPTLCEMLSYTPSSSKDRLF", "snv": [ { "evidence": [ { "id": "rs754124034", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754124034" }, { "id": "rs754124034", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754124034" }, { "id": "rs754124034", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754124034" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897078", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D304", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2064829355", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064829355" }, { "id": "rs2064829355", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064829355" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897076", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D304", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.284.284", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.305.305", "start_pos": 305, "end_pos": 305, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2505828957", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505828957", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs377604605", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377604605", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs377604605", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377604605#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "ECMACSDNTVRAGLTPKFID", "down_seq": "PTLCEMLSYTPSSSKDRLFL", "snv": [ { "evidence": [ { "id": "rs2505828957", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505828957" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897080", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V305", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs377604605", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377604605" }, { "id": "rs377604605", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377604605#frequency_tab" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897079", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V305", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs377604605", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377604605" }, { "id": "rs377604605", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377604605#frequency_tab" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897079", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V305", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.306.306", "start_pos": 306, "end_pos": 306, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1192642291", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1192642291", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1192642291", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1192642291", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs199956743", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199956743", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs199956743", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199956743", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs199956743", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199956743", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs199956743", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199956743#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs199956743", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199956743", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1475612450", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1475612450", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1475612450", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1475612450#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "CMACSDNTVRAGLTPKFIDV", "down_seq": "TLCEMLSYTPSSSKDRLFLP", "snv": [ { "evidence": [ { "id": "rs1192642291", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1192642291" }, { "id": "rs1192642291", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1192642291" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897083", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P306", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs199956743", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199956743" }, { "id": "rs199956743", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199956743" }, { "id": "rs199956743", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199956743" }, { "id": "rs199956743", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199956743#frequency_tab" }, { "id": "rs199956743", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199956743" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897143", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0", "site_lbl": "P306", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs199956743", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199956743" }, { "id": "rs199956743", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199956743" }, { "id": "rs199956743", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199956743" }, { "id": "rs199956743", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199956743#frequency_tab" }, { "id": "rs199956743", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199956743" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897143", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0", "site_lbl": "P306", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1475612450", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1475612450" }, { "id": "rs1475612450", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1475612450#frequency_tab" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897142", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P306", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.286.286", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.307.307", "start_pos": 307, "end_pos": 307, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064840019", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064840019", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064840019", "url": "https://www.ensembl.org/id/rs2064840019", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2064830438", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064830438", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064830438", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064830438", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs769308248", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769308248", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769308248", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769308248", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769308248", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769308248", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs142113673", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142113673", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs142113673", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142113673", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs142113673", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142113673#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs142113673", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142113673", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MACSDNTVRAGLTPKFIDVP", "down_seq": "LCEMLSYTPSSSKDRLFLPT", "snv": [ { "evidence": [ { "id": "rs2064840019", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064840019" }, { "id": "rs2064840019", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064840019" }, { "id": "rs2064830438", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064830438" }, { "id": "rs2064830438", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064830438" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897527", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T307", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs769308248", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769308248" }, { "id": "rs769308248", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769308248" }, { "id": "rs769308248", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769308248" }, { "id": "rs142113673", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142113673" }, { "id": "rs142113673", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142113673" }, { "id": "rs142113673", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142113673#frequency_tab" }, { "id": "rs142113673", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142113673" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897146", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T307", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs142113673", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142113673" }, { "id": "rs142113673", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs142113673" }, { "id": "rs142113673", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs142113673#frequency_tab" }, { "id": "rs142113673", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs142113673" } ], "glycoeffect": [], "sequence_org": "T", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897086", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T307", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.288.288", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.309.309", "start_pos": 309, "end_pos": 309, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1433931750", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1433931750", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1433931750", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1433931750", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "CSDNTVRAGLTPKFIDVPTL", "down_seq": "EMLSYTPSSSKDRLFLPTRS", "snv": [ { "evidence": [ { "id": "rs1433931750", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1433931750" }, { "id": "rs1433931750", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1433931750" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897092", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C309", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.289.289", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.290.290", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.30.30", "start_pos": 30, "end_pos": 30, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1419824964", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1419824964", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1419824964", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1419824964#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1419824964", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1419824964", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1555478118", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555478118", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "SCAVQQYAWGKMGSNSEVAR", "down_seq": "LASSDPLAQIAEDKPYAELW", "snv": [ { "evidence": [ { "id": "rs1419824964", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1419824964" }, { "id": "rs1419824964", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1419824964#frequency_tab" }, { "id": "rs1419824964", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1419824964" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890598", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L30", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1555478118", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555478118" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890599_74890623", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L30", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.311.311", "start_pos": 311, "end_pos": 311, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064829673", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064829673", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064829673", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064829673#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "DNTVRAGLTPKFIDVPTLCE", "down_seq": "LSYTPSSSKDRLFLPTRSQE", "snv": [ { "evidence": [ { "id": "rs2064829673", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064829673" }, { "id": "rs2064829673", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064829673#frequency_tab" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897097", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M311", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.291.291", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.312.312", "start_pos": 312, "end_pos": 312, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs905233208", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs905233208", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs905233208", "url": "https://www.ncbi.nlm.nih.gov/snp/rs905233208#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1356646703", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1356646703", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1356646703", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1356646703#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1356646703", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1356646703", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1258669087", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1258669087", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1258669087", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1258669087#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1258669087", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1258669087", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "NTVRAGLTPKFIDVPTLCEM", "down_seq": "SYTPSSSKDRLFLPTRSQED", "snv": [ { "evidence": [ { "id": "rs905233208", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs905233208" }, { "id": "rs905233208", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs905233208#frequency_tab" }, { "id": "rs1356646703", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1356646703" }, { "id": "rs1356646703", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1356646703#frequency_tab" }, { "id": "rs1356646703", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1356646703" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897544", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L312", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1258669087", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1258669087" }, { "id": "rs1258669087", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1258669087#frequency_tab" }, { "id": "rs1258669087", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1258669087" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897543", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L312", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.313.313", "start_pos": 313, "end_pos": 313, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1000757267", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1000757267", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1000757267", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1000757267#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TVRAGLTPKFIDVPTLCEML", "down_seq": "YTPSSSKDRLFLPTRSQEDP", "snv": [ { "evidence": [ { "id": "rs1000757267", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1000757267" }, { "id": "rs1000757267", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1000757267#frequency_tab" } ], "glycoeffect": [], "sequence_org": "S", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897104", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S313", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.293.293", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.314.314", "start_pos": 314, "end_pos": 314, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064830959", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064830959", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064830959", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064830959#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs748410219", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748410219", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748410219", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748410219", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748410219", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748410219", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2141208628", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141208628", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VRAGLTPKFIDVPTLCEMLS", "down_seq": "TPSSSKDRLFLPTRSQEDPY", "snv": [ { "evidence": [ { "id": "rs2064830959", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064830959" }, { "id": "rs2064830959", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064830959#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897167", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y314", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs748410219", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748410219" }, { "id": "rs748410219", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748410219" }, { "id": "rs748410219", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748410219" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897106", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y314", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2141208628", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141208628" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897167_74897170", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y314", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.294.294", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.315.315", "start_pos": 315, "end_pos": 315, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs370568381", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370568381", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs370568381", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370568381", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs370568381", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370568381#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs370568381", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370568381", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RAGLTPKFIDVPTLCEMLSY", "down_seq": "PSSSKDRLFLPTRSQEDPYL", "snv": [ { "evidence": [ { "id": "rs370568381", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370568381" }, { "id": "rs370568381", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370568381" }, { "id": "rs370568381", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370568381#frequency_tab" }, { "id": "rs370568381", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370568381" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897110", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T315", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.295.295", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.317.317", "start_pos": 317, "end_pos": 317, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1437466115", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1437466115", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1437466115", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1437466115", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GLTPKFIDVPTLCEMLSYTP", "down_seq": "SSKDRLFLPTRSQEDPYLSI", "snv": [ { "evidence": [ { "id": "rs1437466115", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1437466115" }, { "id": "rs1437466115", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1437466115" } ], "glycoeffect": [], "sequence_org": "S", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897116", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S317", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.297.297", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.318.318", "start_pos": 318, "end_pos": 318, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs371471033", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371471033", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371471033", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371471033#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs371471033", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371471033", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LTPKFIDVPTLCEMLSYTPS", "down_seq": "SKDRLFLPTRSQEDPYLSIY", "snv": [ { "evidence": [ { "id": "rs371471033", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371471033" }, { "id": "rs371471033", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371471033#frequency_tab" }, { "id": "rs371471033", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371471033" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897562", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S318", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.298.298", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.319.319", "start_pos": 319, "end_pos": 319, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TPKFIDVPTLCEMLSYTPSS", "down_seq": "KDRLFLPTRSQEDPYLSIYD", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897122", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S319", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.299.299", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.301.301", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.31.31", "start_pos": 31, "end_pos": 31, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753043673", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753043673", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753043673", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753043673", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753043673", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753043673", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs765537697", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765537697", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765537697", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765537697", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765537697", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765537697", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs765537697", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs765537697", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "CAVQQYAWGKMGSNSEVARL", "down_seq": "ASSDPLAQIAEDKPYAELWM", "snv": [ { "evidence": [ { "id": "rs753043673", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753043673" }, { "id": "rs753043673", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753043673" }, { "id": "rs753043673", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753043673" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890602", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L31", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs765537697", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765537697" }, { "id": "rs765537697", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765537697" }, { "id": "rs765537697", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765537697" }, { "id": "rs765537697", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs765537697" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890601", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L31", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs753043673", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753043673" }, { "id": "rs753043673", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753043673" }, { "id": "rs753043673", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753043673" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890602", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L31", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.323.323", "start_pos": 323, "end_pos": 323, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064830172", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064830172", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064830172", "url": "https://www.ensembl.org/id/rs2064830172", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "IDVPTLCEMLSYTPSSSKDR", "down_seq": "FLPTRSQEDPYLSIYDPPVP", "snv": [ { "evidence": [ { "id": "rs2064830172", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064830172" }, { "id": "rs2064830172", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064830172" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897133", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L323", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.303.303", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.324.324", "start_pos": 324, "end_pos": 324, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1276918786", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1276918786", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "DVPTLCEMLSYTPSSSKDRL", "down_seq": "LPTRSQEDPYLSIYDPPVPD", "snv": [ { "evidence": [ { "id": "rs1276918786", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1276918786" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897133CT", "ref_nt": "]", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F324", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.304.304", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.325.325", "start_pos": 325, "end_pos": 325, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1475049428", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1475049428", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1475049428", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1475049428#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1475049428", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1475049428", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1369226974", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1369226974", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1369226974", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1369226974", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2505829213", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505829213", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "VPTLCEMLSYTPSSSKDRLF", "down_seq": "PTRSQEDPYLSIYDPPVPDF", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897139", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "L325", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1475049428", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1475049428" }, { "id": "rs1475049428", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1475049428#frequency_tab" }, { "id": "rs1475049428", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1475049428" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897140", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L325", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1369226974", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1369226974" }, { "id": "rs1369226974", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1369226974" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897139", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L325", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505829213", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505829213" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897139", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L325", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.305.305", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.326.326", "start_pos": 326, "end_pos": 326, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs199956743", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199956743", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs199956743", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199956743", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs199956743", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199956743", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs199956743", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199956743#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs199956743", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199956743", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1475612450", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1475612450", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1475612450", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1475612450#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "PTLCEMLSYTPSSSKDRLFL", "down_seq": "TRSQEDPYLSIYDPPVPDFT", "snv": [ { "evidence": [ { "id": "rs199956743", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199956743" }, { "id": "rs199956743", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199956743" }, { "id": "rs199956743", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199956743" }, { "id": "rs199956743", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199956743#frequency_tab" }, { "id": "rs199956743", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199956743" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897143", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0", "site_lbl": "P326", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs199956743", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199956743" }, { "id": "rs199956743", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199956743" }, { "id": "rs199956743", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199956743" }, { "id": "rs199956743", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199956743#frequency_tab" }, { "id": "rs199956743", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199956743" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897143", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0", "site_lbl": "P326", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1475612450", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1475612450" }, { "id": "rs1475612450", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1475612450#frequency_tab" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897142", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P326", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.306.306", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.327.327", "start_pos": 327, "end_pos": 327, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064830438", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064830438", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064830438", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064830438", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs769308248", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769308248", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769308248", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769308248", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769308248", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769308248", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TLCEMLSYTPSSSKDRLFLP", "down_seq": "RSQEDPYLSIYDPPVPDFTI", "snv": [ { "evidence": [ { "id": "rs2064830438", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064830438" }, { "id": "rs2064830438", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064830438" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897145", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T327", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs769308248", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769308248" }, { "id": "rs769308248", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769308248" }, { "id": "rs769308248", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769308248" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897146", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T327", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.328.328", "start_pos": 328, "end_pos": 328, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs117089191", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs117089191", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs117089191", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs117089191", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs117089191", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs117089191", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs117089191", "url": "https://www.ncbi.nlm.nih.gov/snp/rs117089191#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs117089191", "url": "http://gnomad.broadinstitute.org/awesome?query=rs117089191", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs563261773", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs563261773", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs563261773", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs563261773", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs563261773", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs563261773", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs563261773", "url": "https://www.ncbi.nlm.nih.gov/snp/rs563261773#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs563261773", "url": "http://gnomad.broadinstitute.org/awesome?query=rs563261773", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs563261773", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs563261773", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs117089191", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs117089191", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LCEMLSYTPSSSKDRLFLPT", "down_seq": "SQEDPYLSIYDPPVPDFTIM", "snv": [ { "evidence": [ { "id": "rs117089191", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs117089191" }, { "id": "rs117089191", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs117089191" }, { "id": "rs117089191", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs117089191" }, { "id": "rs117089191", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs117089191#frequency_tab" }, { "id": "rs117089191", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs117089191" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897148", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R328", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs563261773", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs563261773" }, { "id": "rs563261773", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs563261773" }, { "id": "rs563261773", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs563261773" }, { "id": "rs563261773", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs563261773#frequency_tab" }, { "id": "rs563261773", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs563261773" }, { "id": "rs563261773", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs563261773" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897149", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R328", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs117089191", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs117089191" }, { "id": "rs117089191", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs117089191" }, { "id": "rs117089191", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs117089191" }, { "id": "rs117089191", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs117089191#frequency_tab" }, { "id": "rs117089191", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs117089191" }, { "id": "rs117089191", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs117089191" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897148", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R328", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.309.309", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.32.32", "start_pos": 32, "end_pos": 32, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1596440893", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1596440893", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1596440893", "url": "https://www.ensembl.org/id/rs1596440893", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "AVQQYAWGKMGSNSEVARLL", "down_seq": "SSDPLAQIAEDKPYAELWMG", "snv": [ { "evidence": [ { "id": "rs1596440893", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1596440893" }, { "id": "rs1596440893", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1596440893" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890605", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A32", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1596440893", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1596440893" }, { "id": "rs1596440893", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1596440893" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890605", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A32", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.330.330", "start_pos": 330, "end_pos": 330, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs768148327", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768148327", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768148327", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768148327", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs768148327", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768148327", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2141208599", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141208599", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2141208599", "url": "https://www.ensembl.org/id/rs2141208599", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "EMLSYTPSSSKDRLFLPTRS", "down_seq": "EDPYLSIYDPPVPDFTIMKT", "snv": [ { "evidence": [ { "id": "rs768148327", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768148327" }, { "id": "rs768148327", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768148327" }, { "id": "rs768148327", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768148327" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897154", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q330", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2141208599", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141208599" }, { "id": "rs2141208599", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2141208599" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897155", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q330", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.331.331", "start_pos": 331, "end_pos": 331, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1237538373", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1237538373", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1223295146", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1223295146", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1223295146", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1223295146#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1223295146", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1223295146", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1237538373", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1237538373", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1237538373", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1237538373", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1555479423", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555479423", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "MLSYTPSSSKDRLFLPTRSQ", "down_seq": "DPYLSIYDPPVPDFTIMKTE", "snv": [ { "evidence": [ { "id": "rs1237538373", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1237538373" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897217", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E331", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1223295146", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1223295146" }, { "id": "rs1223295146", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1223295146#frequency_tab" }, { "id": "rs1223295146", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1223295146" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897158", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E331", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ] }, { "evidence": [ { "id": "rs1223295146", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1223295146" }, { "id": "rs1223295146", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1223295146#frequency_tab" }, { "id": "rs1223295146", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1223295146" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897158", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E331", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1237538373", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1237538373" }, { "id": "rs1237538373", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1237538373" }, { "id": "rs1237538373", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1237538373" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897217", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E331", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1555479423", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555479423" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897157", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E331", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.332.332", "start_pos": 332, "end_pos": 332, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2505829354", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505829354", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LSYTPSSSKDRLFLPTRSQE", "down_seq": "PYLSIYDPPVPDFTIMKTEV", "snv": [ { "evidence": [ { "id": "rs2505829354", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505829354" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897161", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D332", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.312.312", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.333.333", "start_pos": 333, "end_pos": 333, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2064839792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064839792", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064839792", "url": "https://www.ensembl.org/id/rs2064839792", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2064830862", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064830862", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064830862", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064830862#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2505831279", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505831279", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "SYTPSSSKDRLFLPTRSQED", "down_seq": "YLSIYDPPVPDFTIMKTEVP", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs2064839792", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064839792" }, { "id": "rs2064839792", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064839792" }, { "id": "rs2064830862", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064830862" }, { "id": "rs2064830862", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064830862#frequency_tab" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897163", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P333", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505831279", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505831279" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897516", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P333", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.313.313", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.334.334", "start_pos": 334, "end_pos": 334, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064830959", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064830959", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064830959", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064830959#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2141208628", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141208628", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "YTPSSSKDRLFLPTRSQEDP", "down_seq": "LSIYDPPVPDFTIMKTEVPG", "snv": [ { "evidence": [ { "id": "rs2064830959", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064830959" }, { "id": "rs2064830959", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064830959#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897167", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y334", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2141208628", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141208628" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897167_74897170", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y334", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.314.314", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.335.335", "start_pos": 335, "end_pos": 335, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1453540656", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1453540656", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1453540656", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1453540656#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1453540656", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1453540656", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2505829401", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505829401", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "TPSSSKDRLFLPTRSQEDPY", "down_seq": "SIYDPPVPDFTIMKTEVPGS", "snv": [ { "evidence": [ { "id": "rs1453540656", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1453540656" }, { "id": "rs1453540656", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1453540656#frequency_tab" }, { "id": "rs1453540656", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1453540656" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897169", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L335", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505829401", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505829401" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897167_74897168", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L335", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.315.315", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.336.336", "start_pos": 336, "end_pos": 336, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2064831079", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064831079", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064831079", "url": "https://www.ensembl.org/id/rs2064831079", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2064831079", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2064831079", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs2505829426", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505829426", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2505829304", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505829304", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSSSKDRLFLPTRSQEDPYL", "down_seq": "IYDPPVPDFTIMKTEVPGSV", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897173", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S336", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs2064831079", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064831079" }, { "id": "rs2064831079", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064831079" }, { "id": "rs2064831079", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2064831079" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897173", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S336", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs2505829426", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505829426" }, { "id": "rs2505829304", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505829304" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897170TC", "ref_nt": "]", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S336", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.337.337", "start_pos": 337, "end_pos": 337, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "SSSKDRLFLPTRSQEDPYLS", "down_seq": "YDPPVPDFTIMKTEVPGSVT", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "I", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897177", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "I337", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.317.317", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.338.338", "start_pos": 338, "end_pos": 338, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs774253901", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774253901", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774253901", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774253901", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774253901", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774253901#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774253901", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774253901", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SSKDRLFLPTRSQEDPYLSI", "down_seq": "DPPVPDFTIMKTEVPGSVTE", "snv": [ { "evidence": [ { "id": "rs774253901", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774253901" }, { "id": "rs774253901", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774253901" }, { "id": "rs774253901", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774253901#frequency_tab" }, { "id": "rs774253901", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774253901" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897179", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y338", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs774253901", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774253901" }, { "id": "rs774253901", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774253901" }, { "id": "rs774253901", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774253901#frequency_tab" }, { "id": "rs774253901", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774253901" } ], "glycoeffect": [], "sequence_org": "Y", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897179", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y338", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.318.318", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.339.339", "start_pos": 339, "end_pos": 339, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs575144583", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs575144583", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs575144583", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs575144583", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs575144583", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs575144583", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs575144583", "url": "https://www.ncbi.nlm.nih.gov/snp/rs575144583#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs575144583", "url": "http://gnomad.broadinstitute.org/awesome?query=rs575144583", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1567269332", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567269332", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1567269332", "url": "https://www.ensembl.org/id/rs1567269332", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2505829538", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505829538", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SKDRLFLPTRSQEDPYLSIY", "down_seq": "PPVPDFTIMKTEVPGSVTEY", "snv": [ { "evidence": [ { "id": "rs575144583", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs575144583" }, { "id": "rs575144583", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs575144583" }, { "id": "rs575144583", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs575144583" }, { "id": "rs575144583", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs575144583#frequency_tab" }, { "id": "rs575144583", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs575144583" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897183", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000588697", "site_lbl": "D339", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897182", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "D339", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1567269332", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567269332" }, { "id": "rs1567269332", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1567269332" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897182", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D339", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505829538", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505829538" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897183_74897190delinsACCC", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D339", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.33.33", "start_pos": 33, "end_pos": 33, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs763585470", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763585470", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763585470", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763585470", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763585470", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs763585470", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VQQYAWGKMGSNSEVARLLA", "down_seq": "SDPLAQIAEDKPYAELWMGT", "snv": [ { "evidence": [ { "id": "rs763585470", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763585470" }, { "id": "rs763585470", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763585470" }, { "id": "rs763585470", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs763585470" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890607", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S33", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs763585470", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763585470" }, { "id": "rs763585470", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763585470" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890607", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S33", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74890608", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S33", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.340.340", "start_pos": 340, "end_pos": 340, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760628024", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760628024", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1227125832", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1227125832", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1227125832", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1227125832#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs760628024", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760628024", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760628024", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760628024#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs760628024", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760628024", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "KDRLFLPTRSQEDPYLSIYD", "down_seq": "PVPDFTIMKTEVPGSVTEYK", "snv": [ { "evidence": [ { "id": "rs760628024", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760628024" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897184", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P340", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1227125832", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1227125832" }, { "id": "rs1227125832", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1227125832#frequency_tab" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897185", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P340", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760628024", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760628024" }, { "id": "rs760628024", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760628024" }, { "id": "rs760628024", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760628024#frequency_tab" }, { "id": "rs760628024", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760628024" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897184", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P340", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.341.341", "start_pos": 341, "end_pos": 341, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs765310894", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765310894", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "DRLFLPTRSQEDPYLSIYDP", "down_seq": "VPDFTIMKTEVPGSVTEYKV", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897188", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P341", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs765310894", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765310894" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897188", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P341", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.342.342", "start_pos": 342, "end_pos": 342, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064831861", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064831861", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064831861", "url": "https://www.ensembl.org/id/rs2064831861", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs766568229", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766568229", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs766568229", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766568229", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs766568229", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766568229", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs765310894", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765310894", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1555479441", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555479441", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "RLFLPTRSQEDPYLSIYDPP", "down_seq": "PDFTIMKTEVPGSVTEYKVL", "snv": [ { "evidence": [ { "id": "rs2064831861", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064831861" }, { "id": "rs2064831861", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064831861" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897191", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V342", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs766568229", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766568229" }, { "id": "rs766568229", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766568229" }, { "id": "rs766568229", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766568229" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897190", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V342", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs766568229", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766568229" }, { "id": "rs766568229", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766568229" }, { "id": "rs766568229", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766568229" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897190", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V342", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs765310894", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765310894" }, { "id": "rs1555479441", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555479441" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897188", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V342", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.323.323", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.344.344", "start_pos": 344, "end_pos": 344, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064831922", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064831922", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064831922", "url": "https://www.ensembl.org/id/rs2064831922", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2064831979", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064831979", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064831979", "url": "https://www.ensembl.org/id/rs2064831979", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "FLPTRSQEDPYLSIYDPPVP", "down_seq": "FTIMKTEVPGSVTEYKVLAL", "snv": [ { "evidence": [ { "id": "rs2064831922", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064831922" }, { "id": "rs2064831922", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064831922" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897197", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D344", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2064831979", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064831979" }, { "id": "rs2064831979", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064831979" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897198", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D344", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.324.324", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.345.345", "start_pos": 345, "end_pos": 345, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753928739", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753928739", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753928739", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753928739", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753928739", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753928739#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs753928739", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753928739", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "LPTRSQEDPYLSIYDPPVPD", "down_seq": "TIMKTEVPGSVTEYKVLALD", "snv": [ { "evidence": [ { "id": "rs753928739", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753928739" }, { "id": "rs753928739", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753928739" }, { "id": "rs753928739", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753928739#frequency_tab" }, { "id": "rs753928739", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753928739" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897199", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F345", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.325.325", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.346.346", "start_pos": 346, "end_pos": 346, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1393245343", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1393245343", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1393245343", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1393245343#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1393245343", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1393245343", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2064832138", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064832138", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064832138", "url": "https://www.ensembl.org/id/rs2064832138", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2141208718", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141208718", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PTRSQEDPYLSIYDPPVPDF", "down_seq": "IMKTEVPGSVTEYKVLALDS", "snv": [ { "evidence": [ { "id": "rs1393245343", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1393245343" }, { "id": "rs1393245343", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1393245343#frequency_tab" }, { "id": "rs1393245343", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1393245343" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897202", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T346", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897203", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T346", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs2064832138", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064832138" }, { "id": "rs2064832138", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064832138" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897203", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T346", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2141208718", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141208718" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897200", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T346", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.326.326", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.347.347", "start_pos": 347, "end_pos": 347, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064832233", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064832233", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064832233", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064832233#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2064832233", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064832233", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "TRSQEDPYLSIYDPPVPDFT", "down_seq": "MKTEVPGSVTEYKVLALDSA", "snv": [ { "evidence": [ { "id": "rs2064832233", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064832233" }, { "id": "rs2064832233", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064832233#frequency_tab" }, { "id": "rs2064832233", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064832233" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897206", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I347", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.327.327", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.328.328", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.34.34", "start_pos": 34, "end_pos": 34, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs978284448", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs978284448", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs978284448", "url": "https://www.ncbi.nlm.nih.gov/snp/rs978284448#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs978284448", "url": "http://gnomad.broadinstitute.org/awesome?query=rs978284448", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs952139459", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs952139459", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs952139459", "url": "https://www.ncbi.nlm.nih.gov/snp/rs952139459#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1596440910", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1596440910", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1596440910", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1596440910#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QQYAWGKMGSNSEVARLLAS", "down_seq": "DPLAQIAEDKPYAELWMGTH", "snv": [ { "evidence": [ { "id": "rs978284448", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs978284448" }, { "id": "rs978284448", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs978284448#frequency_tab" }, { "id": "rs978284448", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs978284448" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891485", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S34", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs952139459", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs952139459" }, { "id": "rs952139459", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs952139459#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890611", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S34", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1596440910", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1596440910" }, { "id": "rs1596440910", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1596440910#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890612", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S34", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.350.350", "start_pos": 350, "end_pos": 350, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs116933453", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs116933453", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs116933453", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs116933453", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs116933453", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs116933453", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs116933453", "url": "https://www.ncbi.nlm.nih.gov/snp/rs116933453#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs116933453", "url": "http://gnomad.broadinstitute.org/awesome?query=rs116933453", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1440560558", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1440560558", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1440560558", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1440560558", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QEDPYLSIYDPPVPDFTIMK", "down_seq": "EVPGSVTEYKVLALDSASIL", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs116933453", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs116933453" }, { "id": "rs116933453", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs116933453" }, { "id": "rs116933453", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs116933453" }, { "id": "rs116933453", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs116933453#frequency_tab" }, { "id": "rs116933453", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs116933453" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897215", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T350", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs1440560558", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1440560558" }, { "id": "rs1440560558", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1440560558" } ], "glycoeffect": [], "sequence_org": "T", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897214", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T350", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.330.330", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.351.351", "start_pos": 351, "end_pos": 351, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1237538373", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1237538373", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1237538373", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1237538373", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1237538373", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1237538373", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "EDPYLSIYDPPVPDFTIMKT", "down_seq": "VPGSVTEYKVLALDSASILL", "snv": [ { "evidence": [ { "id": "rs1237538373", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1237538373" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897217", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E351", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs1237538373", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1237538373" }, { "id": "rs1237538373", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1237538373" }, { "id": "rs1237538373", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1237538373" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897217", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E351", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.331.331", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.352.352", "start_pos": 352, "end_pos": 352, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs887001981", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs887001981", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs887001981", "url": "http://gnomad.broadinstitute.org/awesome?query=rs887001981", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs887001981", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs887001981", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "DPYLSIYDPPVPDFTIMKTE", "down_seq": "PGSVTEYKVLALDSASILLM", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs887001981", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs887001981" }, { "id": "rs887001981", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs887001981" }, { "id": "rs887001981", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs887001981" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897512", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V352", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs887001981", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs887001981" }, { "id": "rs887001981", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs887001981" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897512", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V352", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.332.332", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.353.353", "start_pos": 353, "end_pos": 353, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2064839792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064839792", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064839792", "url": "https://www.ensembl.org/id/rs2064839792", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2505831279", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505831279", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "PYLSIYDPPVPDFTIMKTEV", "down_seq": "GSVTEYKVLALDSASILLMV", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897516", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P353", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs2064839792", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064839792" }, { "id": "rs2064839792", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064839792" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897515", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P353", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505831279", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505831279" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897516", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P353", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.333.333", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.354.354", "start_pos": 354, "end_pos": 354, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2505831300", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505831300", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "YLSIYDPPVPDFTIMKTEVP", "down_seq": "SVTEYKVLALDSASILLMVQ", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs2505831300", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505831300" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897519", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G354", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.334.334", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.355.355", "start_pos": 355, "end_pos": 355, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs763169640", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763169640", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763169640", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763169640", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763169640", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763169640#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs763169640", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763169640", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2064839839", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064839839", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LSIYDPPVPDFTIMKTEVPG", "down_seq": "VTEYKVLALDSASILLMVQG", "snv": [ { "evidence": [ { "id": "rs763169640", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763169640" }, { "id": "rs763169640", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763169640" }, { "id": "rs763169640", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763169640#frequency_tab" }, { "id": "rs763169640", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763169640" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897522", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S355", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs763169640", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763169640" }, { "id": "rs763169640", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763169640" }, { "id": "rs763169640", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763169640#frequency_tab" }, { "id": "rs763169640", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763169640" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897522", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S355", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2064839839", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064839839" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897520CT", "ref_nt": "]", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S355", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.335.335", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.356.356", "start_pos": 356, "end_pos": 356, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs764476271", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764476271", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764476271", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764476271", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764476271", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764476271", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "SIYDPPVPDFTIMKTEVPGS", "down_seq": "TEYKVLALDSASILLMVQGT", "snv": [ { "evidence": [ { "id": "rs764476271", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764476271" }, { "id": "rs764476271", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764476271" }, { "id": "rs764476271", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764476271" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897524", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V356", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs764476271", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764476271" }, { "id": "rs764476271", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764476271" }, { "id": "rs764476271", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764476271" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897524", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V356", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.336.336", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.357.357", "start_pos": 357, "end_pos": 357, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064840019", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064840019", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064840019", "url": "https://www.ensembl.org/id/rs2064840019", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IYDPPVPDFTIMKTEVPGSV", "down_seq": "EYKVLALDSASILLMVQGTV", "snv": [ { "evidence": [ { "id": "rs2064840019", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064840019" }, { "id": "rs2064840019", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064840019" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897527", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T357", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.338.338", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.339.339", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.35.35", "start_pos": 35, "end_pos": 35, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1367981360", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1367981360", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1367981360", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1367981360", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs764648534", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764648534", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764648534", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764648534", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764648534", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764648534", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QYAWGKMGSNSEVARLLASS", "down_seq": "PLAQIAEDKPYAELWMGTHP", "snv": [ { "evidence": [ { "id": "rs1367981360", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1367981360" }, { "id": "rs1367981360", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1367981360" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890615", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D35", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74890613", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "D35", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74890613", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D35", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs764648534", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764648534" }, { "id": "rs764648534", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764648534" }, { "id": "rs764648534", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764648534" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890614", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D35", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.360.360", "start_pos": 360, "end_pos": 360, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1399841759", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1399841759", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1399841759", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1399841759#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1399841759", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1399841759", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PPVPDFTIMKTEVPGSVTEY", "down_seq": "VLALDSASILLMVQGTVIAS", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs1399841759", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1399841759" }, { "id": "rs1399841759", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1399841759#frequency_tab" }, { "id": "rs1399841759", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1399841759" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897537", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K360", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.340.340", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.361.361", "start_pos": 361, "end_pos": 361, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs751874530", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751874530", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751874530", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751874530", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751874530", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751874530", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "PVPDFTIMKTEVPGSVTEYK", "down_seq": "LALDSASILLMVQGTVIAST", "snv": [ { "evidence": [ { "id": "rs751874530", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751874530" }, { "id": "rs751874530", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751874530" }, { "id": "rs751874530", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751874530" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897539", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V361", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.362.362", "start_pos": 362, "end_pos": 362, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs905233208", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs905233208", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs905233208", "url": "https://www.ncbi.nlm.nih.gov/snp/rs905233208#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1258669087", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1258669087", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1258669087", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1258669087#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1258669087", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1258669087", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "VPDFTIMKTEVPGSVTEYKV", "down_seq": "ALDSASILLMVQGTVIASTP", "snv": [ { "evidence": [ { "id": "rs905233208", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs905233208" }, { "id": "rs905233208", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs905233208#frequency_tab" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897544", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L362", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1258669087", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1258669087" }, { "id": "rs1258669087", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1258669087#frequency_tab" }, { "id": "rs1258669087", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1258669087" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897543", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L362", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.342.342", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.363.363", "start_pos": 363, "end_pos": 363, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064840301", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064840301", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064840301", "url": "https://www.ensembl.org/id/rs2064840301", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2141209567", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141209567", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PDFTIMKTEVPGSVTEYKVL", "down_seq": "LDSASILLMVQGTVIASTPT", "snv": [ { "evidence": [ { "id": "rs2064840301", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064840301" }, { "id": "rs2064840301", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064840301" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897545", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A363", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2141209567", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141209567" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897545", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A363", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.344.344", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.345.345", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.366.366", "start_pos": 366, "end_pos": 366, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1555479551", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555479551", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1555479551", "url": "https://www.ensembl.org/id/rs1555479551", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TIMKTEVPGSVTEYKVLALD", "down_seq": "ASILLMVQGTVIASTPTTQT", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897555", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S366", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1555479551", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555479551" }, { "id": "rs1555479551", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1555479551" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897554", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S366", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.346.346", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.367.367", "start_pos": 367, "end_pos": 367, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757813144", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757813144", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757813144", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757813144", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757813144", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757813144", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "IMKTEVPGSVTEYKVLALDS", "down_seq": "SILLMVQGTVIASTPTTQTP", "snv": [ { "evidence": [ { "id": "rs757813144", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757813144" }, { "id": "rs757813144", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757813144" }, { "id": "rs757813144", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757813144" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897558", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A367", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.347.347", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.368.368", "start_pos": 368, "end_pos": 368, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs371471033", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371471033", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371471033", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371471033#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs371471033", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371471033", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MKTEVPGSVTEYKVLALDSA", "down_seq": "ILLMVQGTVIASTPTTQTPI", "snv": [ { "evidence": [ { "id": "rs371471033", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371471033" }, { "id": "rs371471033", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371471033#frequency_tab" }, { "id": "rs371471033", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371471033" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897562", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S368", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.36.36", "start_pos": 36, "end_pos": 36, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs750003143", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750003143", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750003143", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750003143", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750003143", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750003143", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2064711019", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064711019", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064711019", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064711019", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "YAWGKMGSNSEVARLLASSD", "down_seq": "LAQIAEDKPYAELWMGTHPR", "snv": [ { "evidence": [ { "id": "rs750003143", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750003143" }, { "id": "rs750003143", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750003143" }, { "id": "rs750003143", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750003143" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890616", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P36", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2064711019", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064711019" }, { "id": "rs2064711019", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064711019" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890617", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P36", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.371.371", "start_pos": 371, "end_pos": 371, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1403486851", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1403486851", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1403486851", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1403486851#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1403486851", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1403486851", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "EVPGSVTEYKVLALDSASIL", "down_seq": "MVQGTVIASTPTTQTPIPLQ", "snv": [ { "evidence": [ { "id": "rs1403486851", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1403486851" }, { "id": "rs1403486851", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1403486851#frequency_tab" }, { "id": "rs1403486851", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1403486851" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897569", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L371", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.351.351", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.372.372", "start_pos": 372, "end_pos": 372, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1398311778", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1398311778", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1398311778", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1398311778", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "VPGSVTEYKVLALDSASILL", "down_seq": "VQGTVIASTPTTQTPIPLQR", "snv": [ { "evidence": [ { "id": "rs1398311778", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1398311778" }, { "id": "rs1398311778", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1398311778" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897573", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M372", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "M", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897572", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "M372", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.352.352", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.373.373", "start_pos": 373, "end_pos": 373, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs781643554", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781643554", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781643554", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781643554", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781643554", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781643554", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs781643554", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs781643554", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "PGSVTEYKVLALDSASILLM", "down_seq": "QGTVIASTPTTQTPIPLQRG", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs781643554", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781643554" }, { "id": "rs781643554", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781643554" }, { "id": "rs781643554", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781643554" }, { "id": "rs781643554", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs781643554" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897575", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V373", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.374.374", "start_pos": 374, "end_pos": 374, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064840759", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064840759", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064840759", "url": "https://www.ensembl.org/id/rs2064840759", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs753458883", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753458883", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753458883", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753458883", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753458883", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753458883#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs753458883", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753458883", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "GSVTEYKVLALDSASILLMV", "down_seq": "GTVIASTPTTQTPIPLQRGG", "snv": [ { "evidence": [ { "id": "rs2064840759", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064840759" }, { "id": "rs2064840759", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064840759" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897578", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q374", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs753458883", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753458883" }, { "id": "rs753458883", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753458883" }, { "id": "rs753458883", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753458883#frequency_tab" }, { "id": "rs753458883", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753458883" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Q", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897580", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Q374", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.354.354", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.375.375", "start_pos": 375, "end_pos": 375, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064840907", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064840907", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064840907", "url": "https://www.ensembl.org/id/rs2064840907", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs148707185", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148707185", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs148707185", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148707185", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs148707185", "url": "https://www.ncbi.nlm.nih.gov/snp/rs148707185#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs148707185", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148707185", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SVTEYKVLALDSASILLMVQ", "down_seq": "TVIASTPTTQTPIPLQRGGV", "snv": [ { "evidence": [ { "id": "rs2064840907", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064840907" }, { "id": "rs2064840907", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064840907" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897582", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G375", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs148707185", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148707185" }, { "id": "rs148707185", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148707185" }, { "id": "rs148707185", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs148707185#frequency_tab" }, { "id": "rs148707185", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148707185" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897581", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G375", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897581", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G375", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.355.355", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.376.376", "start_pos": 376, "end_pos": 376, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1324340168", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1324340168", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1324340168", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1324340168", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1567269757", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567269757", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VTEYKVLALDSASILLMVQG", "down_seq": "VIASTPTTQTPIPLQRGGVL", "snv": [ { "evidence": [ { "id": "rs1324340168", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1324340168" }, { "id": "rs1324340168", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1324340168" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897584", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T376", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1324340168", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1324340168" }, { "id": "rs1324340168", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1324340168" } ], "glycoeffect": [], "sequence_org": "T", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897584", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T376", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1567269757", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567269757" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897585_74897586", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T376", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.356.356", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.377.377", "start_pos": 377, "end_pos": 377, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs747755732", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747755732", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747755732", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747755732", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747755732", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747755732#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs747755732", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747755732", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "TEYKVLALDSASILLMVQGT", "down_seq": "IASTPTTQTPIPLQRGGVLF", "snv": [ { "evidence": [ { "id": "rs747755732", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747755732" }, { "id": "rs747755732", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747755732" }, { "id": "rs747755732", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747755732#frequency_tab" }, { "id": "rs747755732", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747755732" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897587", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0", "site_lbl": "V377", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs747755732", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747755732" }, { "id": "rs747755732", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747755732" }, { "id": "rs747755732", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs747755732#frequency_tab" }, { "id": "rs747755732", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747755732" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897587", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0", "site_lbl": "V377", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.357.357", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.378.378", "start_pos": 378, "end_pos": 378, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1346961642", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1346961642", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1346961642", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1346961642", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs369326210", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369326210", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs369326210", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369326210", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs369326210", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369326210#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs369326210", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369326210", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2505831580", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505831580", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "EYKVLALDSASILLMVQGTV", "down_seq": "ASTPTTQTPIPLQRGGVLFI", "snv": [ { "evidence": [ { "id": "rs1346961642", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1346961642" }, { "id": "rs1346961642", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1346961642" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897592", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I378", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs369326210", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369326210" }, { "id": "rs369326210", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369326210" }, { "id": "rs369326210", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369326210#frequency_tab" }, { "id": "rs369326210", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369326210" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897651", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I378", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505831580", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505831580" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897592", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I378", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.379.379", "start_pos": 379, "end_pos": 379, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs374702385", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374702385", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs374702385", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374702385", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs374702385", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374702385#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs374702385", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374702385", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs374702385", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs374702385", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "YKVLALDSASILLMVQGTVI", "down_seq": "STPTTQTPIPLQRGGVLFIG", "snv": [ { "evidence": [ { "id": "rs374702385", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374702385" }, { "id": "rs374702385", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374702385" }, { "id": "rs374702385", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374702385#frequency_tab" }, { "id": "rs374702385", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374702385" }, { "id": "rs374702385", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs374702385" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897594", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A379", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.37.37", "start_pos": 37, "end_pos": 37, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs755656144", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755656144", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs755656144", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755656144", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs755656144", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755656144", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "AWGKMGSNSEVARLLASSDP", "down_seq": "AQIAEDKPYAELWMGTHPRG", "snv": [ { "evidence": [ { "id": "rs755656144", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755656144" }, { "id": "rs755656144", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755656144" }, { "id": "rs755656144", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755656144" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890619", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L37", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.380.380", "start_pos": 380, "end_pos": 380, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs141660799", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141660799", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs141660799", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs141660799", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs141660799", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141660799", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs141660799", "url": "https://www.ncbi.nlm.nih.gov/snp/rs141660799#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs141660799", "url": "http://gnomad.broadinstitute.org/awesome?query=rs141660799", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1373861722", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1373861722", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KVLALDSASILLMVQGTVIA", "down_seq": "TPTTQTPIPLQRGGVLFIGA", "snv": [ { "evidence": [ { "id": "rs141660799", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141660799" }, { "id": "rs141660799", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs141660799" }, { "id": "rs141660799", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141660799" }, { "id": "rs141660799", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs141660799#frequency_tab" }, { "id": "rs141660799", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs141660799" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897597", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "S380", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1373861722", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1373861722" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897595_74897598", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S380", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.360.360", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.381.381", "start_pos": 381, "end_pos": 381, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs145481549", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145481549", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs145481549", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145481549", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs145481549", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145481549#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs145481549", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145481549", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VLALDSASILLMVQGTVIAS", "down_seq": "PTTQTPIPLQRGGVLFIGAN", "snv": [ { "evidence": [ { "id": "rs145481549", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145481549" }, { "id": "rs145481549", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145481549" }, { "id": "rs145481549", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145481549#frequency_tab" }, { "id": "rs145481549", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145481549" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897600", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T381", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.382.382", "start_pos": 382, "end_pos": 382, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs776426975", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776426975", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776426975", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776426975", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776426975", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776426975#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs776426975", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776426975", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LALDSASILLMVQGTVIAST", "down_seq": "TTQTPIPLQRGGVLFIGANE", "snv": [ { "evidence": [ { "id": "rs776426975", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776426975" }, { "id": "rs776426975", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776426975" }, { "id": "rs776426975", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776426975#frequency_tab" }, { "id": "rs776426975", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776426975" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897603", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P382", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.362.362", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.363.363", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.384.384", "start_pos": 384, "end_pos": 384, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs759461010", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759461010", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759461010", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759461010", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759461010", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759461010", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LDSASILLMVQGTVIASTPT", "down_seq": "QTPIPLQRGGVLFIGANESV", "snv": [ { "evidence": [ { "id": "rs759461010", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759461010" }, { "id": "rs759461010", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759461010" }, { "id": "rs759461010", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759461010" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897609", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T384", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.385.385", "start_pos": 385, "end_pos": 385, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2505831656", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505831656", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "DSASILLMVQGTVIASTPTT", "down_seq": "TPIPLQRGGVLFIGANESVS", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897611", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q385", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs2505831656", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505831656" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897612", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q385", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.386.386", "start_pos": 386, "end_pos": 386, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2141209748", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141209748", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2141209748", "url": "https://www.ensembl.org/id/rs2141209748", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs769768397", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769768397", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769768397", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769768397", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769768397", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769768397#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs769768397", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769768397", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SASILLMVQGTVIASTPTTQ", "down_seq": "PIPLQRGGVLFIGANESVSL", "snv": [ { "evidence": [ { "id": "rs2141209748", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141209748" }, { "id": "rs2141209748", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2141209748" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897615", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T386", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs769768397", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769768397" }, { "id": "rs769768397", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769768397" }, { "id": "rs769768397", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769768397#frequency_tab" }, { "id": "rs769768397", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769768397" } ], "glycoeffect": [], "sequence_org": "T", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897614", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T386", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.366.366", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.387.387", "start_pos": 387, "end_pos": 387, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1401373560", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1401373560", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1401373560", "url": "https://www.ensembl.org/id/rs1401373560", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ASILLMVQGTVIASTPTTQT", "down_seq": "IPLQRGGVLFIGANESVSLK", "snv": [ { "evidence": [ { "id": "rs1401373560", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1401373560" }, { "id": "rs1401373560", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1401373560" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897617", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P387", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897617", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P387", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.367.367", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.388.388", "start_pos": 388, "end_pos": 388, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs775601021", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775601021", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775601021", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775601021", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775601021", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775601021#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs775601021", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775601021", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "SILLMVQGTVIASTPTTQTP", "down_seq": "PLQRGGVLFIGANESVSLKL", "snv": [ { "evidence": [ { "id": "rs775601021", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775601021" }, { "id": "rs775601021", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775601021" }, { "id": "rs775601021", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775601021#frequency_tab" }, { "id": "rs775601021", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775601021" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897620", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I388", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs775601021", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775601021" }, { "id": "rs775601021", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775601021" }, { "id": "rs775601021", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775601021#frequency_tab" }, { "id": "rs775601021", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775601021" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897620", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I388", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.368.368", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.389.389", "start_pos": 389, "end_pos": 389, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1595824816", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1595824816", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1595824816", "url": "https://www.ensembl.org/id/rs1595824816", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2505831709", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505831709", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ILLMVQGTVIASTPTTQTPI", "down_seq": "LQRGGVLFIGANESVSLKLT", "snv": [ { "evidence": [ { "id": "rs1595824816", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1595824816" }, { "id": "rs1595824816", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1595824816" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897624", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P389", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505831709", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505831709" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897624", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P389", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.38.38", "start_pos": 38, "end_pos": 38, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs201217606", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201217606", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201217606", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201217606", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201217606", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201217606#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "WGKMGSNSEVARLLASSDPL", "down_seq": "QIAEDKPYAELWMGTHPRGD", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74890622", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A38", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs201217606", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201217606" }, { "id": "rs201217606", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201217606" }, { "id": "rs201217606", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201217606#frequency_tab" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890623", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "A38", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.391.391", "start_pos": 391, "end_pos": 391, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1375419552", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1375419552", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1375419552", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1375419552", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs764282170", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764282170", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764282170", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764282170", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764282170", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764282170", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "LMVQGTVIASTPTTQTPIPL", "down_seq": "RGGVLFIGANESVSLKLTEP", "snv": [ { "evidence": [ { "id": "rs1375419552", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1375419552" }, { "id": "rs1375419552", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1375419552" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897631", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q391", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs764282170", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764282170" }, { "id": "rs764282170", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764282170" }, { "id": "rs764282170", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764282170" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897630", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q391", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.371.371", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.392.392", "start_pos": 392, "end_pos": 392, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs751962765", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751962765", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751962765", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751962765", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751962765", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751962765#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs751962765", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751962765", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs751962765", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs751962765", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs762164813", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762164813", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762164813", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762164813", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762164813", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762164813#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs762164813", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762164813", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MVQGTVIASTPTTQTPIPLQ", "down_seq": "GGVLFIGANESVSLKLTEPK", "snv": [ { "evidence": [ { "id": "rs751962765", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751962765" }, { "id": "rs751962765", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751962765" }, { "id": "rs751962765", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751962765#frequency_tab" }, { "id": "rs751962765", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751962765" }, { "id": "rs751962765", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs751962765" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897632", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R392", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "somatic", "disease" ] }, { "evidence": [ { "id": "rs762164813", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762164813" }, { "id": "rs762164813", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762164813" }, { "id": "rs762164813", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs762164813#frequency_tab" }, { "id": "rs762164813", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762164813" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897633", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R392", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.372.372", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.393.393", "start_pos": 393, "end_pos": 393, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201815588", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201815588", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201815588", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201815588", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201815588", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201815588", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201815588", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201815588#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201815588", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201815588", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "VQGTVIASTPTTQTPIPLQR", "down_seq": "GVLFIGANESVSLKLTEPKD", "snv": [ { "evidence": [ { "id": "rs201815588", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201815588" }, { "id": "rs201815588", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201815588" }, { "id": "rs201815588", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201815588" }, { "id": "rs201815588", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201815588#frequency_tab" }, { "id": "rs201815588", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201815588" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897636", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "G393", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs201815588", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201815588" }, { "id": "rs201815588", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201815588" }, { "id": "rs201815588", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201815588" }, { "id": "rs201815588", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201815588#frequency_tab" }, { "id": "rs201815588", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201815588" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897636", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "G393", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897635", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G393", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.373.373", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.394.394", "start_pos": 394, "end_pos": 394, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1381312233", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1381312233", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1381312233", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1381312233", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1381312233", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1381312233", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs2064842308", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064842308", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064842308", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064842308#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "QGTVIASTPTTQTPIPLQRG", "down_seq": "VLFIGANESVSLKLTEPKDL", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs1381312233", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1381312233" }, { "id": "rs1381312233", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1381312233" }, { "id": "rs1381312233", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1381312233" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897639", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G394", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs2064842308", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064842308" }, { "id": "rs2064842308", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064842308#frequency_tab" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897638", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G394", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1381312233", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1381312233" }, { "id": "rs1381312233", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1381312233" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897639", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G394", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.374.374", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.395.395", "start_pos": 395, "end_pos": 395, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs968235395", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs968235395", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs968235395", "url": "https://www.ncbi.nlm.nih.gov/snp/rs968235395#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs968235395", "url": "http://gnomad.broadinstitute.org/awesome?query=rs968235395", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs968235395", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs968235395", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "GTVIASTPTTQTPIPLQRGG", "down_seq": "LFIGANESVSLKLTEPKDLL", "snv": [ { "evidence": [ { "id": "rs968235395", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs968235395" }, { "id": "rs968235395", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs968235395#frequency_tab" }, { "id": "rs968235395", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs968235395" }, { "id": "rs968235395", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs968235395" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897641", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V395", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.375.375", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.396.396", "start_pos": 396, "end_pos": 396, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064842502", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064842502", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064842502", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064842502#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "TVIASTPTTQTPIPLQRGGV", "down_seq": "FIGANESVSLKLTEPKDLLI", "snv": [ { "evidence": [ { "id": "rs2064842502", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064842502" }, { "id": "rs2064842502", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064842502#frequency_tab" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897644", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L396", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.376.376", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.416.416", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.397.397", "start_pos": 397, "end_pos": 397, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2064843675", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064843675", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064843675", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064843675#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2064843675", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2064843675", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "VIASTPTTQTPIPLQRGGVL", "down_seq": "IGANESVSLKLTEPKDLLIF", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs2064843675", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064843675" }, { "id": "rs2064843675", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064843675#frequency_tab" }, { "id": "rs2064843675", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2064843675" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "F", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897647", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "F397", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.377.377", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.416.416", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.417.417", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.398.398", "start_pos": 398, "end_pos": 398, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs369326210", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369326210", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs369326210", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369326210", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs369326210", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369326210#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs369326210", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369326210", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "IASTPTTQTPIPLQRGGVLF", "down_seq": "GANESVSLKLTEPKDLLIFR", "snv": [ { "evidence": [ { "id": "rs369326210", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369326210" }, { "id": "rs369326210", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369326210" }, { "id": "rs369326210", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369326210#frequency_tab" }, { "id": "rs369326210", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369326210" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897651", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I398", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs369326210", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369326210" }, { "id": "rs369326210", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369326210" }, { "id": "rs369326210", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369326210#frequency_tab" }, { "id": "rs369326210", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369326210" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897651", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I398", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.378.378", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.379.379", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.416.416", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.418.418", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1265892778", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1265892778", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1265892778", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1265892778#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1265892778", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1265892778", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs770421382", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770421382", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770421382", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770421382", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs770421382", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770421382#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs770421382", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770421382", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "MA", "down_seq": "PRVFPLSCAVQQYAWGKMGS", "snv": [ { "evidence": [ { "id": "rs1265892778", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1265892778" }, { "id": "rs1265892778", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1265892778#frequency_tab" }, { "id": "rs1265892778", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1265892778" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890081", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A3", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs770421382", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770421382" }, { "id": "rs770421382", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770421382" }, { "id": "rs770421382", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770421382#frequency_tab" }, { "id": "rs770421382", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770421382" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890080", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A3", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs770421382", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770421382" }, { "id": "rs770421382", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770421382" }, { "id": "rs770421382", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770421382#frequency_tab" }, { "id": "rs770421382", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770421382" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890080", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A3", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P34949-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.401.401", "start_pos": 401, "end_pos": 401, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs201263032", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201263032", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201263032", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201263032", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs201263032", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201263032", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs201263032", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201263032#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201263032", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201263032", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TPTTQTPIPLQRGGVLFIGA", "down_seq": "ESVSLKLTEPKDLLIFRACC", "snv": [ { "evidence": [ { "id": "rs201263032", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201263032" }, { "id": "rs201263032", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs201263032" }, { "id": "rs201263032", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201263032" }, { "id": "rs201263032", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201263032#frequency_tab" }, { "id": "rs201263032", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201263032" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897660", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "N401", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.381.381", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.416.416", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.418.418", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.419.419", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.420.420", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.402.402", "start_pos": 402, "end_pos": 402, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs863225086", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs863225086", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs863225086", "url": "https://www.ncbi.nlm.nih.gov/snp/rs863225086#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1381474522", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1381474522", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1381474522", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1381474522#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1381474522", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1381474522", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "PTTQTPIPLQRGGVLFIGAN", "down_seq": "SVSLKLTEPKDLLIFRACCL", "snv": [ { "evidence": [ { "id": "rs863225086", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs863225086" }, { "id": "rs863225086", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs863225086#frequency_tab" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897663", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E402", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1381474522", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1381474522" }, { "id": "rs1381474522", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1381474522#frequency_tab" }, { "id": "rs1381474522", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1381474522" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897662", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E402", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1381474522", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1381474522" }, { "id": "rs1381474522", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1381474522#frequency_tab" }, { "id": "rs1381474522", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1381474522" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897662", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E402", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.382.382", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.416.416", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.418.418", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.419.419", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.420.420", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.403.403", "start_pos": 403, "end_pos": 403, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs916251037", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs916251037", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs916251037", "url": "https://www.ncbi.nlm.nih.gov/snp/rs916251037#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs916251037", "url": "http://gnomad.broadinstitute.org/awesome?query=rs916251037", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TTQTPIPLQRGGVLFIGANE", "down_seq": "VSLKLTEPKDLLIFRACCLL", "snv": [ { "evidence": [ { "id": "rs916251037", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs916251037" }, { "id": "rs916251037", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs916251037#frequency_tab" }, { "id": "rs916251037", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs916251037" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897665", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S403", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.416.416", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.418.418", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.419.419", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.420.420", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.404.404", "start_pos": 404, "end_pos": 404, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064843020", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064843020", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064843020", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064843020#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2064843020", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064843020", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "TQTPIPLQRGGVLFIGANES", "down_seq": "SLKLTEPKDLLIFRACCLL", "snv": [ { "evidence": [ { "id": "rs2064843020", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064843020" }, { "id": "rs2064843020", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064843020#frequency_tab" }, { "id": "rs2064843020", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064843020" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897668", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V404", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.384.384", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.416.416", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.418.418", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.419.419", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.420.420", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.405.405", "start_pos": 405, "end_pos": 405, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QTPIPLQRGGVLFIGANESV", "down_seq": "LKLTEPKDLLIFRACCLL", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897672", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S405", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.416.416", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.418.418", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.419.419", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.420.420", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.406.406", "start_pos": 406, "end_pos": 406, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs949249403", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs949249403", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs949249403", "url": "https://www.ncbi.nlm.nih.gov/snp/rs949249403#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "TPIPLQRGGVLFIGANESVS", "down_seq": "KLTEPKDLLIFRACCLL", "snv": [ { "evidence": [ { "id": "rs949249403", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs949249403" }, { "id": "rs949249403", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs949249403#frequency_tab" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897675", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L406", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.386.386", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.416.416", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.418.418", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.419.419", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.420.420", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.407.407", "start_pos": 407, "end_pos": 407, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1318127045", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1318127045", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1318127045", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1318127045#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PIPLQRGGVLFIGANESVSL", "down_seq": "LTEPKDLLIFRACCLL", "snv": [ { "evidence": [ { "id": "rs1318127045", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1318127045" }, { "id": "rs1318127045", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1318127045#frequency_tab" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897678", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K407", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.387.387", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.388.388", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.416.416", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.418.418", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.419.419", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.420.420", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.409.409", "start_pos": 409, "end_pos": 409, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1394939460", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1394939460", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1394939460", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1394939460", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2064843322", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064843322", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064843322", "url": "https://www.ensembl.org/id/rs2064843322", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PLQRGGVLFIGANESVSLKL", "down_seq": "EPKDLLIFRACCLL", "snv": [ { "evidence": [ { "id": "rs1394939460", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1394939460" }, { "id": "rs1394939460", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1394939460" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897684", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T409", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2064843322", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064843322" }, { "id": "rs2064843322", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064843322" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897683", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T409", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.389.389", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.416.416", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.418.418", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.419.419", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.420.420", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.40.40", "start_pos": 40, "end_pos": 40, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1395810504", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1395810504", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1395810504", "url": "https://www.ensembl.org/id/rs1395810504", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1057516466", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057516466", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "KMGSNSEVARLLASSDPLAQ", "down_seq": "AEDKPYAELWMGTHPRGDAK", "snv": [ { "evidence": [ { "id": "rs1395810504", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1395810504" }, { "id": "rs1395810504", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1395810504" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890630", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I40", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1057516466", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1057516466" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890630", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I40", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.411.411", "start_pos": 411, "end_pos": 411, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs147817691", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs147817691", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs147817691", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs147817691", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs147817691", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs147817691", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs147817691", "url": "https://www.ncbi.nlm.nih.gov/snp/rs147817691#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs147817691", "url": "http://gnomad.broadinstitute.org/awesome?query=rs147817691", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs147817691", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs147817691", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "QRGGVLFIGANESVSLKLTE", "down_seq": "KDLLIFRACCLL", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs147817691", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs147817691" }, { "id": "rs147817691", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs147817691" }, { "id": "rs147817691", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs147817691" }, { "id": "rs147817691", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs147817691#frequency_tab" }, { "id": "rs147817691", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs147817691" }, { "id": "rs147817691", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs147817691" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897690", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P411", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.391.391", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.392.392", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.416.416", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.418.418", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.419.419", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.420.420", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.413.413", "start_pos": 413, "end_pos": 413, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757104332", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757104332", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757104332", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757104332", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757104332", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757104332#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs757104332", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757104332", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GGVLFIGANESVSLKLTEPK", "down_seq": "LLIFRACCLL", "snv": [ { "evidence": [ { "id": "rs757104332", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757104332" }, { "id": "rs757104332", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757104332" }, { "id": "rs757104332", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757104332#frequency_tab" }, { "id": "rs757104332", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757104332" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897696", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D413", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897695", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D413", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.393.393", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.394.394", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.395.395", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.416.416", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.418.418", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.419.419", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.420.420", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.416.416", "start_pos": 416, "end_pos": 416, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1172970106", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1172970106", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1172970106", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1172970106#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2141209973", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141209973", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2141209973", "url": "https://www.ensembl.org/id/rs2141209973", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "LFIGANESVSLKLTEPKDLL", "down_seq": "FRACCLL", "snv": [ { "evidence": [ { "id": "rs1172970106", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1172970106" }, { "id": "rs1172970106", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1172970106#frequency_tab" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897704", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I416", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2141209973", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2141209973" }, { "id": "rs2141209973", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2141209973" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897706", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I416", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.396.396", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.418.418", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.419.419", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.420.420", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.417.417", "start_pos": 417, "end_pos": 417, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064843675", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064843675", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064843675", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064843675#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "FIGANESVSLKLTEPKDLLI", "down_seq": "RACCLL", "snv": [ { "evidence": [ { "id": "rs2064843675", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064843675" }, { "id": "rs2064843675", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064843675#frequency_tab" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897707", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F417", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.397.397", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.416.416", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.418.418", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.419.419", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.420.420", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.418.418", "start_pos": 418, "end_pos": 418, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs745824777", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745824777", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs745824777", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745824777", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs745824777", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745824777#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs745824777", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745824777", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs745824777", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs745824777", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs863225087", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs863225087", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs863225087", "url": "https://www.ncbi.nlm.nih.gov/snp/rs863225087#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs863225087", "url": "http://gnomad.broadinstitute.org/awesome?query=rs863225087", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs863225087", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs863225087", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IGANESVSLKLTEPKDLLIF", "down_seq": "ACCLL", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs745824777", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745824777" }, { "id": "rs745824777", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745824777" }, { "id": "rs745824777", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745824777#frequency_tab" }, { "id": "rs745824777", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745824777" }, { "id": "rs745824777", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs745824777" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897710", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R418", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs863225087", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs863225087" }, { "id": "rs863225087", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs863225087#frequency_tab" }, { "id": "rs863225087", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs863225087" }, { "id": "rs863225087", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs863225087" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74897711", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R418", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.398.398", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.416.416", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.419.419", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.420.420", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.419.419", "start_pos": 419, "end_pos": 419, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1438367897", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1438367897", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1438367897", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1438367897", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1324976385", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1324976385", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1324976385", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1324976385", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1324976385", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1324976385", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GANESVSLKLTEPKDLLIFR", "down_seq": "CCLL", "snv": [ { "evidence": [ { "id": "rs1438367897", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1438367897" }, { "id": "rs1438367897", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1438367897" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897713", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A419", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1324976385", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1324976385" }, { "id": "rs1324976385", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1324976385" }, { "id": "rs1324976385", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1324976385" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897714", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A419", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.416.416", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.418.418", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.420.420", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs779821212", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779821212", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779821212", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779821212", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779821212", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779821212#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779821212", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779821212", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs372226364", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372226364", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs372226364", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372226364", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs372226364", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372226364#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs372226364", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372226364", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2505811515", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505811515", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "MGSNSEVARLLASSDPLAQI", "down_seq": "EDKPYAELWMGTHPRGDAKI", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs779821212", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779821212" }, { "id": "rs779821212", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779821212" }, { "id": "rs779821212", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779821212#frequency_tab" }, { "id": "rs779821212", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779821212" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74890631", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A41", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs372226364", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372226364" }, { "id": "rs372226364", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372226364" }, { "id": "rs372226364", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372226364#frequency_tab" }, { "id": "rs372226364", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372226364" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890632", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A41", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505811515", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505811515" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890632", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A41", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.420.420", "start_pos": 420, "end_pos": 420, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1555479632", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555479632", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1555479632", "url": "https://www.ensembl.org/id/rs1555479632", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs776052964", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776052964", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776052964", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776052964", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "ANESVSLKLTEPKDLLIFRA", "down_seq": "CLL", "snv": [ { "evidence": [ { "id": "rs1555479632", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1555479632" }, { "id": "rs1555479632", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1555479632" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897718", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C420", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs776052964", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776052964" }, { "id": "rs776052964", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776052964" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74897717", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C420", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.403.403", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.405.405", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.406.406", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.407.407", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.409.409", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.411.411", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.413.413", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.416.416", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.417.417", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.418.418", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.419.419", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1316039664", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1316039664", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1316039664", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1316039664#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1316039664", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1316039664", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "GSNSEVARLLASSDPLAQIA", "down_seq": "DKPYAELWMGTHPRGDAKIL", "snv": [ { "evidence": [ { "id": "rs1316039664", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1316039664" }, { "id": "rs1316039664", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1316039664#frequency_tab" }, { "id": "rs1316039664", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1316039664" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890634", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E42", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.43.43", "start_pos": 43, "end_pos": 43, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1293697697", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1293697697", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1293697697", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1293697697#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1293697697", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1293697697", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SNSEVARLLASSDPLAQIAE", "down_seq": "KPYAELWMGTHPRGDAKILD", "snv": [ { "evidence": [ { "id": "rs1293697697", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1293697697" }, { "id": "rs1293697697", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1293697697#frequency_tab" }, { "id": "rs1293697697", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1293697697" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890637", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D43", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1293697697", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1293697697" }, { "id": "rs1293697697", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1293697697#frequency_tab" }, { "id": "rs1293697697", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1293697697" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890637", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D43", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1435677254", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1435677254", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1435677254", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1435677254", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1221660842", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1221660842", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1221660842", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1221660842#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1221660842", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1221660842", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2505811546", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505811546", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "SEVARLLASSDPLAQIAEDK", "down_seq": "YAELWMGTHPRGDAKILDNR", "snv": [ { "evidence": [ { "id": "rs1435677254", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1435677254" }, { "id": "rs1435677254", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1435677254" }, { "id": "rs1221660842", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1221660842" }, { "id": "rs1221660842", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1221660842#frequency_tab" }, { "id": "rs1221660842", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1221660842" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891517", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P45", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2505811546", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505811546" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890640_74890643", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P45", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.46.46", "start_pos": 46, "end_pos": 46, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1246142183", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1246142183", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1246142183", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1246142183", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "EVARLLASSDPLAQIAEDKP", "down_seq": "AELWMGTHPRGDAKILDNRI", "snv": [ { "evidence": [ { "id": "rs1246142183", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1246142183" }, { "id": "rs1246142183", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1246142183" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890646", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y46", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1246142183", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1246142183" }, { "id": "rs1246142183", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1246142183" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890646", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y46", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.47.47", "start_pos": 47, "end_pos": 47, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1179088321", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1179088321", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1179088321", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1179088321#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1179088321", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1179088321", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs201856169", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201856169", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs201856169", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201856169#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs201856169", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201856169", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VARLLASSDPLAQIAEDKPY", "down_seq": "ELWMGTHPRGDAKILDNRIS", "snv": [ { "evidence": [ { "id": "rs1179088321", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1179088321" }, { "id": "rs1179088321", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1179088321#frequency_tab" }, { "id": "rs1179088321", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1179088321" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890650", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A47", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs201856169", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs201856169" }, { "id": "rs201856169", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs201856169#frequency_tab" }, { "id": "rs201856169", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs201856169" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890649", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A47", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.48.48", "start_pos": 48, "end_pos": 48, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "ARLLASSDPLAQIAEDKPYA", "down_seq": "LWMGTHPRGDAKILDNRISQ", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74890652", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E48", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.49.49", "start_pos": 49, "end_pos": 49, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs926396606", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs926396606", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs926396606", "url": "https://www.ncbi.nlm.nih.gov/snp/rs926396606#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "RLLASSDPLAQIAEDKPYAE", "down_seq": "WMGTHPRGDAKILDNRISQK", "snv": [ { "evidence": [ { "id": "rs926396606", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs926396606" }, { "id": "rs926396606", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs926396606#frequency_tab" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891379", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L49", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.29.29", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.4.4", "start_pos": 4, "end_pos": 4, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1567263775", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567263775", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1567263775", "url": "https://www.ensembl.org/id/rs1567263775", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs143982014", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143982014", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs143982014", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs143982014", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs143982014", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143982014", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs143982014", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143982014#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs143982014", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143982014", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "MAA", "down_seq": "RVFPLSCAVQQYAWGKMGSN", "snv": [ { "evidence": [ { "id": "rs1567263775", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567263775" }, { "id": "rs1567263775", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1567263775" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890084", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P4", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1567263775", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567263775" }, { "id": "rs1567263775", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1567263775" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890084", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P4", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs143982014", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143982014" }, { "id": "rs143982014", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs143982014" }, { "id": "rs143982014", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs143982014" }, { "id": "rs143982014", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs143982014#frequency_tab" }, { "id": "rs143982014", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs143982014" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890083", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000981162", "site_lbl": "P4", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P34949-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.50.50", "start_pos": 50, "end_pos": 50, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1406722622", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1406722622", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1406722622", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1406722622", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1366088975", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1366088975", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1366088975", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1366088975", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "LLASSDPLAQIAEDKPYAEL", "down_seq": "MGTHPRGDAKILDNRISQKT", "snv": [ { "evidence": [ { "id": "rs1406722622", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1406722622" }, { "id": "rs1406722622", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1406722622" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891384", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W50", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1366088975", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1366088975" }, { "id": "rs1366088975", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1366088975" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891382", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W50", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.30.30", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.51.51", "start_pos": 51, "end_pos": 51, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752339342", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752339342", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752339342", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752339342", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759060141", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759060141", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759060141", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759060141", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759060141", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759060141", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs764835081", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764835081", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764835081", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764835081", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764835081", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764835081", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "LASSDPLAQIAEDKPYAELW", "down_seq": "GTHPRGDAKILDNRISQKTL", "snv": [ { "evidence": [ { "id": "rs752339342", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752339342" }, { "id": "rs752339342", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752339342" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891387", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M51", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs759060141", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759060141" }, { "id": "rs759060141", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759060141" }, { "id": "rs759060141", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759060141" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891385", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M51", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs764835081", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764835081" }, { "id": "rs764835081", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764835081" }, { "id": "rs764835081", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764835081" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891386", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M51", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.31.31", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.54.54", "start_pos": 54, "end_pos": 54, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757990859", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757990859", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757990859", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757990859", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757990859", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757990859#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs757990859", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757990859", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1596442107", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1596442107", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1596442107", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1596442107#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "SDPLAQIAEDKPYAELWMGT", "down_seq": "PRGDAKILDNRISQKTLSQW", "snv": [ { "evidence": [ { "id": "rs757990859", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757990859" }, { "id": "rs757990859", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757990859" }, { "id": "rs757990859", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757990859#frequency_tab" }, { "id": "rs757990859", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757990859" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891394", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "H54", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1596442107", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1596442107" }, { "id": "rs1596442107", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1596442107#frequency_tab" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891395", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H54", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1596442107", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1596442107" }, { "id": "rs1596442107", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1596442107#frequency_tab" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891395", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H54", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs757990859", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757990859" }, { "id": "rs757990859", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757990859" }, { "id": "rs757990859", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757990859#frequency_tab" }, { "id": "rs757990859", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757990859" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891394", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "H54", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.34.34", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.55.55", "start_pos": 55, "end_pos": 55, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs751320033", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751320033", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751320033", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751320033", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751320033", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751320033#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs751320033", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751320033", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "DPLAQIAEDKPYAELWMGTH", "down_seq": "RGDAKILDNRISQKTLSQWI", "snv": [ { "evidence": [ { "id": "rs751320033", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751320033" }, { "id": "rs751320033", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751320033" }, { "id": "rs751320033", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751320033#frequency_tab" }, { "id": "rs751320033", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751320033" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891397", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P55", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.56.56", "start_pos": 56, "end_pos": 56, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Genomic organization of the human phosphomannose isomerase (MPI) gene and mutation analysis in patients with congenital disorders of glycosylation type Ib (CDG-Ib).", "journal": "Human mutation", "date": "2000", "authors": "Schollen E, Dorland L, de Koning TJ, Van Diggelen OP, Huijmans JG, Marquardt T, Babovic-Vuksanovic D, Patterson M, Imtiaz F, Winchester B, Adamowicz M, Pronicka E, Freeze H, Matthijs G", "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" }, { "database": "Reactome", "id": "R-HSA-446205", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-446205" }, { "database": "dbSNP", "id": "rs104894489", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs104894489" }, { "database": "dbSNP", "id": "rs786204593", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs786204593" } ], "reference": [ { "type": "PubMed", "id": "10980531", "url": "https://glygen.org/publication/PubMed/10980531" } ] } ], "crossref": [ { "id": "rs757168691", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757168691", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757168691", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757168691", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757168691", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757168691#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs757168691", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757168691", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs200452019", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200452019", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200452019", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200452019", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs200452019", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200452019", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200452019", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200452019#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200452019", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200452019", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs786204593", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs786204593", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "10980531", "url": "https://glygen.org/publication/PubMed/10980531", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PLAQIAEDKPYAELWMGTHP", "down_seq": "GDAKILDNRISQKTLSQWIA", "snv": [ { "evidence": [ { "id": "rs757168691", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757168691" }, { "id": "rs757168691", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757168691" }, { "id": "rs757168691", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757168691#frequency_tab" }, { "id": "rs757168691", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757168691" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891400", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R56", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs200452019", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200452019" }, { "id": "rs200452019", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200452019" }, { "id": "rs200452019", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200452019" }, { "id": "rs200452019", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200452019#frequency_tab" }, { "id": "rs200452019", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200452019" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891401", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000392465", "site_lbl": "R56", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs786204593", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs786204593" }, { "id": "10980531", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/10980531" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891400", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R56", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.36.36", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P34949-1.57.57", "start_pos": 57, "end_pos": 57, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs750510350", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750510350", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750510350", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750510350", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750510350", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750510350#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs750510350", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750510350", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1225376562", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225376562", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1225376562", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1225376562", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1225376562", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1225376562", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "LAQIAEDKPYAELWMGTHPR", "down_seq": "DAKILDNRISQKTLSQWIAE", "snv": [ { "evidence": [ { "id": "rs750510350", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750510350" }, { "id": "rs750510350", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750510350" }, { "id": "rs750510350", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750510350#frequency_tab" }, { "id": "rs750510350", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750510350" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891404", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G57", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs1225376562", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225376562" }, { "id": "rs1225376562", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1225376562" }, { "id": "rs1225376562", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1225376562" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74891403", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G57", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs750510350", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750510350" }, { "id": "rs750510350", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750510350" }, { "id": "rs750510350", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750510350#frequency_tab" }, { "id": "rs750510350", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750510350" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891404", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G57", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.59.59", "start_pos": 59, "end_pos": 59, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QIAEDKPYAELWMGTHPRGD", "down_seq": "KILDNRISQKTLSQWIAENQ", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74891410", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A59", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.5.5", "start_pos": 5, "end_pos": 5, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1452559752", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1452559752", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1452559752", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1452559752#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1452559752", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1452559752", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs759385120", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759385120", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759385120", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759385120", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759385120", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759385120#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs759385120", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759385120", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs759385120", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs759385120", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MAAP", "down_seq": "VFPLSCAVQQYAWGKMGSNS", "snv": [ { "evidence": [ { "id": "rs1452559752", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1452559752" }, { "id": "rs1452559752", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1452559752#frequency_tab" }, { "id": "rs1452559752", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1452559752" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890086", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R5", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs759385120", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759385120" }, { "id": "rs759385120", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759385120" }, { "id": "rs759385120", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759385120#frequency_tab" }, { "id": "rs759385120", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759385120" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890087", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R5", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs759385120", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759385120" }, { "id": "rs759385120", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759385120" }, { "id": "rs759385120", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759385120#frequency_tab" }, { "id": "rs759385120", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759385120" }, { "id": "rs759385120", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs759385120" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890087", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R5", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74890087", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R5", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P34949-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.60.60", "start_pos": 60, "end_pos": 60, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "IAEDKPYAELWMGTHPRGDA", "down_seq": "ILDNRISQKTLSQWIAENQD", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74891414", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K60", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.40.40", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.61.61", "start_pos": 61, "end_pos": 61, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1450529645", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1450529645", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1450529645", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1450529645", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "AEDKPYAELWMGTHPRGDAK", "down_seq": "LDNRISQKTLSQWIAENQDS", "snv": [ { "evidence": [ { "id": "rs1450529645", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1450529645" }, { "id": "rs1450529645", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1450529645" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891415", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I61", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.62.62", "start_pos": 62, "end_pos": 62, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs780479484", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780479484", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780479484", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780479484", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780479484", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780479484#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs780479484", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780479484", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs780479484", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs780479484", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs2505813576", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505813576", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "EDKPYAELWMGTHPRGDAKI", "down_seq": "DNRISQKTLSQWIAENQDSL", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs780479484", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780479484" }, { "id": "rs780479484", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780479484" }, { "id": "rs780479484", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780479484#frequency_tab" }, { "id": "rs780479484", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780479484" }, { "id": "rs780479484", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs780479484" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74891418", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "L62", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs780479484", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780479484" }, { "id": "rs780479484", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780479484" }, { "id": "rs780479484", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs780479484#frequency_tab" }, { "id": "rs780479484", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780479484" }, { "id": "rs2505813576", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505813576" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891418", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L62", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.64.64", "start_pos": 64, "end_pos": 64, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1468326053", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1468326053", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1468326053", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1468326053#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1468326053", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1468326053", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KPYAELWMGTHPRGDAKILD", "down_seq": "RISQKTLSQWIAENQDSLGS", "snv": [ { "evidence": [ { "id": "rs1468326053", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1468326053" }, { "id": "rs1468326053", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1468326053#frequency_tab" }, { "id": "rs1468326053", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1468326053" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891424", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N64", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1468326053", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1468326053" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891424", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N64", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.65.65", "start_pos": 65, "end_pos": 65, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs749533638", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749533638", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs749533638", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749533638", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs749533638", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749533638", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs749533638", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs749533638", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs768931867", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768931867", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768931867", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768931867", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs768931867", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768931867", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs768931867", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs768931867", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PYAELWMGTHPRGDAKILDN", "down_seq": "ISQKTLSQWIAENQDSLGSK", "snv": [ { "evidence": [ { "id": "rs749533638", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749533638" }, { "id": "rs749533638", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749533638" }, { "id": "rs749533638", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749533638" }, { "id": "rs749533638", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs749533638" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891427", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R65", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs749533638", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749533638" }, { "id": "rs749533638", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749533638" }, { "id": "rs749533638", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749533638" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891427", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R65", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs768931867", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768931867" }, { "id": "rs768931867", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768931867" }, { "id": "rs768931867", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768931867" }, { "id": "rs768931867", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs768931867" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74891428", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R65", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs768931867", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768931867" }, { "id": "rs768931867", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768931867" }, { "id": "rs768931867", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768931867" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891428", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R65", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs768931867", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768931867" }, { "id": "rs768931867", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768931867" }, { "id": "rs768931867", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768931867" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891428", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R65", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs749533638", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749533638" }, { "id": "rs749533638", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749533638" }, { "id": "rs749533638", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749533638" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891427", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R65", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.45.45", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.67.67", "start_pos": 67, "end_pos": 67, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2505813641", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505813641", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AELWMGTHPRGDAKILDNRI", "down_seq": "QKTLSQWIAENQDSLGSKVK", "snv": [ { "evidence": [ { "id": "rs2505813641", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505813641" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891433", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S67", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.68.68", "start_pos": 68, "end_pos": 68, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "ELWMGTHPRGDAKILDNRIS", "down_seq": "KTLSQWIAENQDSLGSKVKD", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Q", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74891437", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Q68", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.69.69", "start_pos": 69, "end_pos": 69, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2505813657", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505813657", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LWMGTHPRGDAKILDNRISQ", "down_seq": "TLSQWIAENQDSLGSKVKDT", "snv": [ { "evidence": [ { "id": "rs2505813657", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505813657" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891440", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K69", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.6.6", "start_pos": 6, "end_pos": 6, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064708499", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064708499", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064708499", "url": "https://www.ensembl.org/id/rs2064708499", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs946927722", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs946927722", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs946927722", "url": "https://www.ncbi.nlm.nih.gov/snp/rs946927722#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "MAAPR", "down_seq": "FPLSCAVQQYAWGKMGSNSE", "snv": [ { "evidence": [ { "id": "rs2064708499", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064708499" }, { "id": "rs2064708499", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064708499" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890527", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V6", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs946927722", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs946927722" }, { "id": "rs946927722", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs946927722#frequency_tab" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890089", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V6", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs946927722", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs946927722" }, { "id": "rs946927722", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs946927722#frequency_tab" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890089", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V6", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P34949-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.71.71", "start_pos": 71, "end_pos": 71, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2505815561", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505815561", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "MGTHPRGDAKILDNRISQKT", "down_seq": "SQWIAENQDSLGSKVKDTFN", "snv": [ { "evidence": [ { "id": "rs2505815561", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505815561" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892677", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L71", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.72.72", "start_pos": 72, "end_pos": 72, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs146699267", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146699267", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs146699267", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs146699267", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs146699267", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146699267", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs146699267", "url": "https://www.ncbi.nlm.nih.gov/snp/rs146699267#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs146699267", "url": "http://gnomad.broadinstitute.org/awesome?query=rs146699267", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs146699267", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs146699267", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GTHPRGDAKILDNRISQKTL", "down_seq": "QWIAENQDSLGSKVKDTFNG", "snv": [ { "evidence": [ { "id": "rs146699267", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146699267" }, { "id": "rs146699267", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs146699267" }, { "id": "rs146699267", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs146699267" }, { "id": "rs146699267", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs146699267#frequency_tab" }, { "id": "rs146699267", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs146699267" }, { "id": "rs146699267", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs146699267" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891448", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S72", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "somatic", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.74.74", "start_pos": 74, "end_pos": 74, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2505813674", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505813674", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "HPRGDAKILDNRISQKTLSQ", "down_seq": "IAENQDSLGSKVKDTFNGNL", "snv": [ { "evidence": [ { "id": "rs2505813674", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505813674" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891456", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W74", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.76.76", "start_pos": 76, "end_pos": 76, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs568011248", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs568011248", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs568011248", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs568011248", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs568011248", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs568011248", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs568011248", "url": "http://gnomad.broadinstitute.org/awesome?query=rs568011248", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "RGDAKILDNRISQKTLSQWI", "down_seq": "ENQDSLGSKVKDTFNGNLPF", "snv": [ { "evidence": [ { "id": "rs568011248", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs568011248" }, { "id": "rs568011248", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs568011248" }, { "id": "rs568011248", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs568011248" }, { "id": "rs568011248", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs568011248" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891460", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "A76", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.56.56", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.77.77", "start_pos": 77, "end_pos": 77, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064725514", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064725514", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064725514", "url": "https://www.ensembl.org/id/rs2064725514", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "GDAKILDNRISQKTLSQWIA", "down_seq": "NQDSLGSKVKDTFNGNLPFL", "snv": [ { "evidence": [ { "id": "rs2064725514", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064725514" }, { "id": "rs2064725514", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064725514" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891463", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E77", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs759032019", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759032019", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759032019", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759032019", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759032019", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759032019", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DAKILDNRISQKTLSQWIAE", "down_seq": "QDSLGSKVKDTFNGNLPFLF", "snv": [ { "evidence": [ { "id": "rs759032019", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759032019" }, { "id": "rs759032019", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759032019" }, { "id": "rs759032019", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759032019" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891468", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N78", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.80.80", "start_pos": 80, "end_pos": 80, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs769362236", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769362236", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769362236", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769362236", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769362236", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769362236#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs769362236", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769362236", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1444877183", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1444877183", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1444877183", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1444877183#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1444877183", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1444877183", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "KILDNRISQKTLSQWIAENQ", "down_seq": "SLGSKVKDTFNGNLPFLFKV", "snv": [ { "evidence": [ { "id": "rs769362236", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769362236" }, { "id": "rs769362236", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769362236" }, { "id": "rs769362236", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769362236#frequency_tab" }, { "id": "rs769362236", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769362236" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891474", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D80", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74891473", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "D80", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1444877183", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1444877183" }, { "id": "rs1444877183", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1444877183#frequency_tab" }, { "id": "rs1444877183", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1444877183" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891472", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D80", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" }, { "id": "rs1444877183", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1444877183" }, { "id": "rs1444877183", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1444877183#frequency_tab" }, { "id": "rs1444877183", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1444877183" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74891472", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D80", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.83.83", "start_pos": 83, "end_pos": 83, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "DNRISQKTLSQWIAENQDSL", "down_seq": "SKVKDTFNGNLPFLFKVLSV", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74891482", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G83", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.84.84", "start_pos": 84, "end_pos": 84, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs978284448", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs978284448", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs978284448", "url": "https://www.ncbi.nlm.nih.gov/snp/rs978284448#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs978284448", "url": "http://gnomad.broadinstitute.org/awesome?query=rs978284448", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NRISQKTLSQWIAENQDSLG", "down_seq": "KVKDTFNGNLPFLFKVLSVE", "snv": [ { "evidence": [ { "id": "rs978284448", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs978284448" }, { "id": "rs978284448", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs978284448#frequency_tab" }, { "id": "rs978284448", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs978284448" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891485", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S84", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.86.86", "start_pos": 86, "end_pos": 86, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs774917281", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774917281", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774917281", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774917281", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774917281", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774917281#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774917281", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774917281", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "ISQKTLSQWIAENQDSLGSK", "down_seq": "KDTFNGNLPFLFKVLSVETP", "snv": [ { "evidence": [ { "id": "rs774917281", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774917281" }, { "id": "rs774917281", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774917281" }, { "id": "rs774917281", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774917281#frequency_tab" }, { "id": "rs774917281", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774917281" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891490", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V86", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.88.88", "start_pos": 88, "end_pos": 88, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064725963", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064725963", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064725963", "url": "https://www.ensembl.org/id/rs2064725963", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs868127074", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs868127074", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QKTLSQWIAENQDSLGSKVK", "down_seq": "TFNGNLPFLFKVLSVETPLS", "snv": [ { "evidence": [ { "id": "rs2064725963", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064725963" }, { "id": "rs2064725963", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2064725963" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891496", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D88", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs868127074", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs868127074" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891498", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D88", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.8.8", "start_pos": 8, "end_pos": 8, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2064708581", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064708581", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064708581", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064708581", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "MAAPRVF", "down_seq": "LSCAVQQYAWGKMGSNSEVA", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74890533", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P8", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs2064708581", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064708581" }, { "id": "rs2064708581", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064708581" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74890532", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P8", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P34949-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.1.1", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.11.11", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.14.14", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.21.21", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.28.28", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.90.90", "start_pos": 90, "end_pos": 90, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2505813810", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505813810", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1207645277", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1207645277", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1207645277", "url": "https://www.ensembl.org/id/rs1207645277", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "TLSQWIAENQDSLGSKVKDT", "down_seq": "NGNLPFLFKVLSVETPLSIQ", "snv": [ { "evidence": [ { "id": "rs2505813810", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505813810" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891503", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F90", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1207645277", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1207645277" }, { "id": "rs1207645277", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1207645277" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891502", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F90", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.71.71", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.92.92", "start_pos": 92, "end_pos": 92, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1195848550", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1195848550", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1195848550", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1195848550", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SQWIAENQDSLGSKVKDTFN", "down_seq": "NLPFLFKVLSVETPLSIQAH", "snv": [ { "evidence": [ { "id": "rs1195848550", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1195848550" }, { "id": "rs1195848550", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1195848550" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891508", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G92", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.93.93", "start_pos": 93, "end_pos": 93, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs762629491", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762629491", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762629491", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762629491", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762629491", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762629491", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QWIAENQDSLGSKVKDTFNG", "down_seq": "LPFLFKVLSVETPLSIQAHP", "snv": [ { "evidence": [ { "id": "rs762629491", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762629491" }, { "id": "rs762629491", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762629491" }, { "id": "rs762629491", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762629491" } ], "glycoeffect": [], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891513", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N93", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.94.94", "start_pos": 94, "end_pos": 94, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064726297", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064726297", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064726297", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064726297", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "WIAENQDSLGSKVKDTFNGN", "down_seq": "PFLFKVLSVETPLSIQAHPN", "snv": [ { "evidence": [ { "id": "rs2064726297", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064726297" }, { "id": "rs2064726297", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064726297" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891515", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L94", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.95.95", "start_pos": 95, "end_pos": 95, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1435677254", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1435677254", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1435677254", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1435677254", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "IAENQDSLGSKVKDTFNGNL", "down_seq": "FLFKVLSVETPLSIQAHPNK", "snv": [ { "evidence": [ { "id": "rs1435677254", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1435677254" }, { "id": "rs1435677254", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1435677254" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891517", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P95", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.96.96", "start_pos": 96, "end_pos": 96, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2505813839", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505813839", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "AENQDSLGSKVKDTFNGNLP", "down_seq": "LFKVLSVETPLSIQAHPNKE", "snv": [ { "evidence": [ { "id": "rs2505813839", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2505813839" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891521", "ref_nt": "l", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F96", "disease": [ { "disease_id": "DOID:0080554", "recommended_name": { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation Ib", "description": "A congenital disorder of glycosylation I that is characterized by protein-losing enteropathy, cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin, protein C and S deficiency, low anti-thrombine III levels and has_material_basis_in compound heterozygous mutation in the gene encoding mannosephosphate isomerase on chromosome 15q24." }, "synonyms": [ { "id": "DOID:0080554", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080554", "name": "congenital disorder of glycosylation 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-congenital disorder of glycosylation", "description": "MPI-CDG is a form of congenital disorders of N-linked glycosylation, characterized by cyclic vomiting, profound hypoglycemia, failure to thrive, liver fibrosis, gastrointestinal complications (protein-losing enteropathy with hypoalbuminaemia, life-threatening intestinal bleeding of diffuse origin), and thrombotic events (protein C and S deficiency, low anti-thrombine III levels), whereas neurological development and cognitive capacity is usually normal. The clinical course is variable even within families. The disease is caused by loss of function of the gene MPI (15q24.1)." }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG-Ib", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate deficient glycoprotein syndrome type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type 1b", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation type IB", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "phosphomannose isomerase deficiency", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "CDG gastrointestinal type", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "MPI-CDG (CDG-Ib)", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "SLSJ syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "Saguenay Lac Saint Jean syndrome", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "carbohydrate-deficient glycoprotein syndrome type 1B", "description": "" }, { "id": "MONDO:0011257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257", "name": "congenital disorder of glycosylation, type IB", "description": "" }, { "id": "MIM:602579", "resource": "MIM", "url": "https://www.omim.org/entry/602579", "name": "Congenital disorder of glycosylation 1B", "description": "Congenital disorder of glycosylation 1B" } ], "unlinked_id_list": [], "evidence": [ { "id": "0011257", "database": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011257" }, { "id": "602579", "database": "MIM", "url": "https://www.omim.org/entry/602579" }, { "id": "MPI", "database": "Genomics England", "url": "https://panelapp.genomicsengland.co.uk/panels/25/gene/MPI/#!details" }, { "id": "4351", "database": "GlyCosmos", "url": "https://glycosmos.org/glycogenes/show/4351#disease" }, { "id": "0080554", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080554" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.97.97", "start_pos": 97, "end_pos": 97, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P34949", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs377074383", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377074383", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs377074383", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377074383", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs377074383", "url": "http://gnomad.broadinstitute.org/awesome?query=rs377074383", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "ENQDSLGSKVKDTFNGNLPF", "down_seq": "FKVLSVETPLSIQAHPNKEL", "snv": [ { "evidence": [ { "id": "P34949", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P34949" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis).", "chr_id": "15", "chr_pos": "74891523", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "L97", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs377074383", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377074383" }, { "id": "rs377074383", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377074383" }, { "id": "rs377074383", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs377074383" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74892664", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L97", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P34949-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.99.99", "start_pos": 99, "end_pos": 99, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2064726523", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064726523", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2064726523", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064726523#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2064726523", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064726523", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "QDSLGSKVKDTFNGNLPFLF", "down_seq": "VLSVETPLSIQAHPNKELAE", "snv": [ { "evidence": [ { "id": "rs2064726523", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2064726523" }, { "id": "rs2064726523", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2064726523#frequency_tab" }, { "id": "rs2064726523", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2064726523" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, carbohydrate synthesis and metabolism/nucleotide synthesis.", "chr_id": "15", "chr_pos": "74891530", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K99", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P34949-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P34949-1.108.108", "start_pos": 108, "end_pos": 108, "uniprot_canonical_ac": "P34949-1", "length": 423, "uniprot_id": "MPI_HUMAN", "protein_name": "Mannose-6-phosphate isomerase", "refseq_ac": "NP_001276085", "refseq_name": "mannose-6-phosphate isomerase isoform 3", "gene_name": "MPI", "gene_names_uniprotkb": "MPI; PMI1", "gene_names_refseq": "CDG1B; MPI; PMI1; PMI", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.", "journal": "Journal of proteomics", "date": "2014", "authors": "Bian Y, Song C, Cheng K, Dong M, Wang F, Huang J, Sun D, Wang L, Ye M, Zou H", "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" }, { "database": "iPTMnet", "id": "P34949", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P34949" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] } ], "crossref": [ { "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P34949", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P34949", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DTFNGNLPFLFKVLSVETPL", "down_seq": "IQAHPNKELAEKLHLQAPQH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P34949", "url": "https://www.uniprot.org/uniprotkb/P34949" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "P34949", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P34949" } ], "site_lbl": "Ser108" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "103", "end_pos": "103" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "122", "end_pos": "122" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "133", "end_pos": "133" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "146", "end_pos": "146" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "158", "end_pos": "158" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "163", "end_pos": "163" }, { "start_pos": "164", "end_pos": "164" }, { "start_pos": "166", "end_pos": "166" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "168", "end_pos": "168" }, { "start_pos": "169", "end_pos": "169" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "190", "end_pos": "190" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "196", "end_pos": "196" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "1", "end_pos": "1" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "201", "end_pos": "201" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "210", "end_pos": "210" }, { "start_pos": "211", "end_pos": "211" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "214", "end_pos": "214" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "21", "end_pos": "21" }, { "start_pos": "220", "end_pos": "220" }, { "start_pos": "221", "end_pos": "221" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "224", "end_pos": "224" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "227", "end_pos": "227" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "233", "end_pos": "233" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "236", "end_pos": "236" }, { "start_pos": "237", "end_pos": "237" }, { "start_pos": "238", "end_pos": "238" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "240", "end_pos": "240" }, { "start_pos": "241", "end_pos": "241" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "247", "end_pos": "247" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "256", "end_pos": "256" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "258", "end_pos": "258" }, { "start_pos": "260", "end_pos": "260" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "262", "end_pos": "262" }, { "start_pos": "263", "end_pos": "263" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "272", "end_pos": "272" }, { "start_pos": "273", "end_pos": "273" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "277", "end_pos": "277" }, { "start_pos": "278", "end_pos": "278" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "282", "end_pos": "282" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "288", "end_pos": "288" }, { "start_pos": "289", "end_pos": "289" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "293", "end_pos": "293" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "295", "end_pos": "295" }, { "start_pos": "297", "end_pos": "297" }, { "start_pos": "298", "end_pos": "298" }, { "start_pos": "299", "end_pos": "299" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "303", "end_pos": "303" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "312", "end_pos": "312" }, { "start_pos": "313", "end_pos": "313" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "315", "end_pos": "315" }, { "start_pos": "317", "end_pos": "317" }, { "start_pos": "318", "end_pos": "318" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "324", "end_pos": "324" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "326", "end_pos": "326" }, { "start_pos": "327", "end_pos": "327" }, { "start_pos": "328", "end_pos": "328" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "330", "end_pos": "330" }, { "start_pos": "331", "end_pos": "331" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "334", "end_pos": "334" }, { "start_pos": "335", "end_pos": "335" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "339", "end_pos": "339" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "344", "end_pos": "344" }, { "start_pos": "345", "end_pos": "345" }, { "start_pos": "346", "end_pos": "346" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "351", "end_pos": "351" }, { "start_pos": "352", "end_pos": "352" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "355", "end_pos": "355" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "362", "end_pos": "362" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "368", "end_pos": "368" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "371", "end_pos": "371" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "374", "end_pos": "374" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "379", "end_pos": "379" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "381", "end_pos": "381" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "387", "end_pos": "387" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "392", "end_pos": "392" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "395", "end_pos": "395" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "398", "end_pos": "398" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "403", "end_pos": "403" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "406", "end_pos": "406" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "413", "end_pos": "413" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "418", "end_pos": "418" }, { "start_pos": "419", "end_pos": "419" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "56", "end_pos": "56" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "95", "end_pos": "95" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "108", "end_pos": "108" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P34949-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P34949-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P34949-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P34949-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P34949-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P34949-1.95.95", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P34949-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P34949-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P34949-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P34949-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P34949-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P34949-1.102.102", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P34949-1.103.103", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P34949-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P34949-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P34949-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P34949-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P34949-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P34949-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P34949-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P34949-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P34949-1.117.117", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P34949-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P34949-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P34949-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P34949-1.121.121", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P34949-1.122.122", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P34949-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P34949-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P34949-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P34949-1.128.128", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6WVG3-1.47.47", "start_pos": 47, "end_pos": 47, "uniprot_canonical_ac": "Q6WVG3-1", "length": 327, "uniprot_id": "KCD12_MOUSE", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_808383", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "Kctd12", "gene_names_uniprotkb": "Kctd12; Pfet1", "gene_names_refseq": "Kctd12; Pfet1; Pfetin", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "GLY_001153", "url": "https://data.glygen.org/GLY_001153", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AEPPLFPDIVELNVGGQVYV", "down_seq": "RRCTVVSVPDSLLWRMFTQQ", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr47", "evidence": [ { "id": "GLY_001153", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001153" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "202", "end_pos": "202" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6WVG3-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q6WVG3-1", "length": 327, "uniprot_id": "KCD12_MOUSE", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_808383", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "Kctd12", "gene_names_uniprotkb": "Kctd12; Pfet1", "gene_names_refseq": "Kctd12; Pfet1; Pfetin", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "O-GlcNAcylation regulates dopamine neuron function, survival and degeneration in Parkinson disease.", "journal": "Brain : a journal of neurology", "date": "2020", "authors": "Lee BE, Kim HY, Kim HJ, Jeong H, Kim BG, Lee HE, Lee J, Kim HB, Lee SE, Yang YR, Yi EC, Hanover JA, Myung K, Suh PG, Kwon T, Kim JI", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6WVG3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6WVG3" } ], "reference": [ { "type": "PubMed", "id": "33300544", "url": "https://glygen.org/publication/PubMed/33300544" } ] } ], "crossref": [ { "id": "33300544", "url": "https://glygen.org/publication/PubMed/33300544", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6WVG3", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6WVG3", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "33300544", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33300544" }, { "id": "Q6WVG3", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6WVG3" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "202", "end_pos": "202" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6WVG3-1.119.119", "start_pos": 119, "end_pos": 119, "uniprot_canonical_ac": "Q6WVG3-1", "length": 327, "uniprot_id": "KCD12_MOUSE", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_808383", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "Kctd12", "gene_names_uniprotkb": "Kctd12; Pfet1", "gene_names_refseq": "Kctd12; Pfet1; Pfetin", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Large-scale identification and evolution indexing of tyrosine phosphorylation sites from murine brain.", "journal": "Journal of proteome research", "date": "2008", "authors": "Ballif BA, Carey GR, Sunyaev SR, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" }, { "database": "iPTMnet", "id": "Q6WVG3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6WVG3" } ], "reference": [ { "type": "PubMed", "id": "18034455", "url": "https://glygen.org/publication/PubMed/18034455" } ] } ], "crossref": [ { "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18034455", "url": "https://glygen.org/publication/PubMed/18034455", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6WVG3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6WVG3", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LQLVLPDYFPERSRLQREAE", "down_seq": "FELPELVRRLGAPQQPGPGP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" }, { "database": "PubMed", "id": "18034455", "url": "https://glygen.org/publication/PubMed/18034455" }, { "database": "iPTMnet", "id": "Q6WVG3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6WVG3" } ], "site_lbl": "Tyr119" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "202", "end_pos": "202" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6WVG3-1.153.153", "start_pos": 153, "end_pos": 153, "uniprot_canonical_ac": "Q6WVG3-1", "length": 327, "uniprot_id": "KCD12_MOUSE", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_808383", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "Kctd12", "gene_names_uniprotkb": "Kctd12; Pfet1", "gene_names_refseq": "Kctd12; Pfet1; Pfetin", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Phosphoproteomic analysis of the developing mouse brain.", "journal": "Molecular & cellular proteomics : MCP", "date": "2004", "authors": "Ballif BA, Villen J, Beausoleil SA, Schwartz D, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" }, { "database": "iPTMnet", "id": "Q6WVG3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6WVG3" } ], "reference": [ { "type": "PubMed", "id": "15345747", "url": "https://glygen.org/publication/PubMed/15345747" } ] }, { "title": "A tissue-specific atlas of mouse protein phosphorylation and expression.", "journal": "Cell", "date": "2010", "authors": "Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villen J, Haas W, Sowa ME, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" }, { "database": "iPTMnet", "id": "Q6WVG3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6WVG3" } ], "reference": [ { "type": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" } ] } ], "crossref": [ { "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15345747", "url": "https://glygen.org/publication/PubMed/15345747", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6WVG3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6WVG3", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QQPGPGPPPPHSRRGVHKEG", "down_seq": "LGDELLPLGYAEPEPQEGAS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" }, { "database": "PubMed", "id": "15345747", "url": "https://glygen.org/publication/PubMed/15345747" }, { "database": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" }, { "database": "iPTMnet", "id": "Q6WVG3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6WVG3" } ], "site_lbl": "Ser153" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "202", "end_pos": "202" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "Q6WVG3-1.173.173", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6WVG3-1.173.173", "start_pos": 173, "end_pos": 173, "uniprot_canonical_ac": "Q6WVG3-1", "length": 327, "uniprot_id": "KCD12_MOUSE", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_808383", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "Kctd12", "gene_names_uniprotkb": "Kctd12; Pfet1", "gene_names_refseq": "Kctd12; Pfet1; Pfetin", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "A tissue-specific atlas of mouse protein phosphorylation and expression.", "journal": "Cell", "date": "2010", "authors": "Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villen J, Haas W, Sowa ME, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" }, { "database": "iPTMnet", "id": "Q6WVG3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6WVG3" } ], "reference": [ { "type": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" } ] } ], "crossref": [ { "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6WVG3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6WVG3", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SLGDELLPLGYAEPEPQEGA", "down_seq": "AGAPSPTLELASRSPSGGAA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" }, { "database": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" }, { "database": "iPTMnet", "id": "Q6WVG3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6WVG3" } ], "site_lbl": "Ser173" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "202", "end_pos": "202" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6WVG3-1.153.153", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6WVG3-1.187.187", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6WVG3-1.187.187", "start_pos": 187, "end_pos": 187, "uniprot_canonical_ac": "Q6WVG3-1", "length": 327, "uniprot_id": "KCD12_MOUSE", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_808383", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "Kctd12", "gene_names_uniprotkb": "Kctd12; Pfet1", "gene_names_refseq": "Kctd12; Pfet1; Pfetin", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EPQEGASAGAPSPTLELASR", "down_seq": "PSGGAAGPLLTPSQSLDGSR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" } ], "site_lbl": "Ser187" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "202", "end_pos": "202" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6WVG3-1.173.173", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6WVG3-1.198.198", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6WVG3-1.202.202", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6WVG3-1.198.198", "start_pos": 198, "end_pos": 198, "uniprot_canonical_ac": "Q6WVG3-1", "length": 327, "uniprot_id": "KCD12_MOUSE", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_808383", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "Kctd12", "gene_names_uniprotkb": "Kctd12; Pfet1", "gene_names_refseq": "Kctd12; Pfet1; Pfetin", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "A tissue-specific atlas of mouse protein phosphorylation and expression.", "journal": "Cell", "date": "2010", "authors": "Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villen J, Haas W, Sowa ME, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" }, { "database": "iPTMnet", "id": "Q6WVG3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6WVG3" } ], "reference": [ { "type": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" } ] }, { "title": "Large-scale phosphorylation analysis of mouse liver.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Villen J, Beausoleil SA, Gerber SA, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" }, { "database": "iPTMnet", "id": "Q6WVG3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6WVG3" } ], "reference": [ { "type": "PubMed", "id": "17242355", "url": "https://glygen.org/publication/PubMed/17242355" } ] } ], "crossref": [ { "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17242355", "url": "https://glygen.org/publication/PubMed/17242355", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6WVG3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6WVG3", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SPTLELASRSPSGGAAGPLL", "down_seq": "PSQSLDGSRRSGYITIGYRG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" }, { "database": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" }, { "database": "PubMed", "id": "17242355", "url": "https://glygen.org/publication/PubMed/17242355" }, { "database": "iPTMnet", "id": "Q6WVG3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6WVG3" } ], "site_lbl": "Thr198" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "202", "end_pos": "202" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q6WVG3-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6WVG3-1.202.202", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6WVG3-1.202.202", "start_pos": 202, "end_pos": 202, "uniprot_canonical_ac": "Q6WVG3-1", "length": 327, "uniprot_id": "KCD12_MOUSE", "protein_name": "BTB/POZ domain-containing protein KCTD12", "refseq_ac": "NP_808383", "refseq_name": "BTB/POZ domain-containing protein KCTD12", "gene_name": "Kctd12", "gene_names_uniprotkb": "Kctd12; Pfet1", "gene_names_refseq": "Kctd12; Pfet1; Pfetin", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "A tissue-specific atlas of mouse protein phosphorylation and expression.", "journal": "Cell", "date": "2010", "authors": "Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villen J, Haas W, Sowa ME, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" }, { "database": "iPTMnet", "id": "Q6WVG3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6WVG3" } ], "reference": [ { "type": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" } ] } ], "crossref": [ { "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6WVG3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6WVG3", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ELASRSPSGGAAGPLLTPSQ", "down_seq": "LDGSRRSGYITIGYRGSYTI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6WVG3", "url": "https://www.uniprot.org/uniprotkb/Q6WVG3" }, { "database": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" }, { "database": "iPTMnet", "id": "Q6WVG3", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6WVG3" } ], "site_lbl": "Ser202" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "47", "end_pos": "47" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "119", "end_pos": "119" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "202", "end_pos": "202" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6WVG3-1.187.187", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6WVG3-1.198.198", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q91VM9-1.311.311", "start_pos": 311, "end_pos": 311, "uniprot_canonical_ac": "Q91VM9-1", "length": 330, "uniprot_id": "IPYR2_MOUSE", "protein_name": "Inorganic pyrophosphatase 2, mitochondrial", "refseq_ac": "NP_001280570", "refseq_name": "inorganic pyrophosphatase 2, mitochondrial isoform 2 precursor", "gene_name": "Ppa2", "gene_names_uniprotkb": "Ppa2", "gene_names_refseq": "1110013G13Rik; Ppa2; Sid6306", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q91VM9", "url": "https://www.uniprot.org/uniprotkb/Q91VM9" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "GLY_001153", "url": "https://data.glygen.org/GLY_001153", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "CDSPFHCTMEEARSLVESVP", "down_seq": "PSMNKESNVEEEVWHFLRN", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr311", "evidence": [ { "id": "GLY_001153", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001153" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" } ] }, { "type": "snv", "site_list": [ { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q91VM9-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q91VM9-1", "length": 330, "uniprot_id": "IPYR2_MOUSE", "protein_name": "Inorganic pyrophosphatase 2, mitochondrial", "refseq_ac": "NP_001280570", "refseq_name": "inorganic pyrophosphatase 2, mitochondrial isoform 2 precursor", "gene_name": "Ppa2", "gene_names_uniprotkb": "Ppa2", "gene_names_refseq": "1110013G13Rik; Ppa2; Sid6306", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q91VM9", "url": "https://www.uniprot.org/uniprotkb/Q91VM9" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Differential Detection of O-GlcNAcylated proteins in the heart using antibodies.", "journal": "Analytical biochemistry", "date": "2023-10-01", "authors": "Narayanan Bhargavi, Zahra Fiddia, Reeves Russell A, Aggarwal Akanksha, O'Meally Robert N, Henry Roger K, Craven Megan, Jacobson Avital, Cole Robert N, Kohr Mark J, Umapathi Priya, Zachara Natasha E", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q91VM9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q91VM9" } ], "reference": [ { "type": "PubMed", "id": "37507081", "url": "https://glygen.org/publication/PubMed/37507081" } ] }, { "title": "The Small Molecule 2-Azido-2-deoxy-glucose Is a Metabolic Chemical Reporter of O-GlcNAc Modifications in Mammalian Cells, Revealing an Unexpected Promiscuity of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2017", "authors": "Zaro BW, Batt AR, Chuh KN, Navarro MX, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q91VM9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q91VM9" } ], "reference": [ { "type": "PubMed", "id": "28135057", "url": "https://glygen.org/publication/PubMed/28135057" } ] }, { "title": "Identification of O-GlcNAc modification targets in mouse retinal pericytes: implication of p53 in pathogenesis of diabetic retinopathy.", "journal": "PloS one", "date": "2014", "authors": "Gurel Z, Zaro BW, Pratt MR, Sheibani N", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q91VM9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q91VM9" } ], "reference": [ { "type": "PubMed", "id": "24788674", "url": "https://glygen.org/publication/PubMed/24788674" } ] }, { "title": "The New Chemical Reporter 6-Alkynyl-6-deoxy-GlcNAc Reveals O-GlcNAc Modification of the Apoptotic Caspases That Can Block the Cleavage/Activation of Caspase-8.", "journal": "Journal of the American Chemical Society", "date": "2017", "authors": "Chuh KN, Batt AR, Zaro BW, Darabedian N, Marotta NP, Brennan CK, Amirhekmat A, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q91VM9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q91VM9" } ], "reference": [ { "type": "PubMed", "id": "28528544", "url": "https://glygen.org/publication/PubMed/28528544" } ] } ], "crossref": [ { "id": "37507081", "url": "https://glygen.org/publication/PubMed/37507081", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q91VM9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q91VM9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28135057", "url": "https://glygen.org/publication/PubMed/28135057", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24788674", "url": "https://glygen.org/publication/PubMed/24788674", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28528544", "url": "https://glygen.org/publication/PubMed/28528544", "database": "PubMed", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "37507081", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37507081" }, { "id": "Q91VM9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q91VM9" }, { "id": "28135057", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28135057" }, { "id": "24788674", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24788674" }, { "id": "28528544", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28528544" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" } ] }, { "type": "snv", "site_list": [ { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q91VM9-1.87.87", "start_pos": 87, "end_pos": 87, "uniprot_canonical_ac": "Q91VM9-1", "length": 330, "uniprot_id": "IPYR2_MOUSE", "protein_name": "Inorganic pyrophosphatase 2, mitochondrial", "refseq_ac": "NP_001280570", "refseq_name": "inorganic pyrophosphatase 2, mitochondrial isoform 2 precursor", "gene_name": "Ppa2", "gene_names_uniprotkb": "Ppa2", "gene_names_refseq": "1110013G13Rik; Ppa2; Sid6306", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q91VM9", "url": "https://www.uniprot.org/uniprotkb/Q91VM9" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "rs3393554556", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3393554556", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "CKEEHDIPRKKARNDEYENL", "down_seq": "NMVVEIPRWTNAKMEIATEE", "snv": [ { "evidence": [ { "id": "rs3393554556", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3393554556" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLF->NLS).", "chr_id": "3", "chr_pos": "133032416", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F87", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "311", "end_pos": "311" } ] }, { "type": "snv", "site_list": [ { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q60980-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "Q60980-1", "length": 344, "uniprot_id": "KLF3_MOUSE", "protein_name": "Krueppel-like factor 3", "refseq_ac": "NP_032479", "refseq_name": "Krueppel-like factor 3", "gene_name": "Klf3", "gene_names_uniprotkb": "Klf3; Bklf", "gene_names_refseq": "9930027G08Rik; Bklf; Klf3; Tef-2", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Chemoproteomic and Transcriptomic Analysis Reveals that O-GlcNAc Regulates Mouse Embryonic Stem Cell Fate through the Pluripotency Network.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2023-02-27", "authors": "Hao Yi, Li Xiang, Qin Ke, Shi Yujie, He Yanwen, Zhang Che, Cheng Bo, Zhang Xiwen, Hu Guangyu, Liang Shuyu, Tang Qi, Chen Xing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q60980", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q60980" }, { "database": "O-GlcNAc Atlas", "id": "Q60980", "url": "https://oglcnac.org/atlas/detail/Q60980" } ], "reference": [ { "type": "PubMed", "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467" } ] }, { "title": "O-GlcNAcylation of nuclear proteins in the mouse liver exhibit daily oscillations that are influenced by meal timing.", "journal": "PLoS biology", "date": "2025-09", "authors": "Liu Xianhui, Cai Yao D, Hou Chunyan, Liu Xu, Luo Youcheng, Mendiola Aron Judd P, Xu Xuehan, Luo Yige, Zheng Haiyan, Zhao Caifeng, Chen Ching-Hsuan, Zhang Yong, Xiang Yang K, Ma Junfeng, Chiu Joanna C", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q60980", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q60980" } ], "reference": [ { "type": "PubMed", "id": "40997131", "url": "https://glygen.org/publication/PubMed/40997131" } ] }, { "title": "Novel Antibodies for the Simple and Efficient Enrichment of Native O-GlcNAc Modified Peptides.", "journal": "Molecular & cellular proteomics : MCP", "date": "2021", "authors": "Burt RA, Dejanovic B, Peckham HJ, Lee KA, Li X, Ounadjela JR, Rao A, Malaker SA, Carr SA, Myers SA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q60980", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q60980" } ], "reference": [ { "type": "PubMed", "id": "34678516", "url": "https://glygen.org/publication/PubMed/34678516" } ] } ], "crossref": [ { "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q60980", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q60980", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "40997131", "url": "https://glygen.org/publication/PubMed/40997131", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34678516", "url": "https://glygen.org/publication/PubMed/34678516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q60980", "url": "https://oglcnac.org/atlas/detail/Q60980", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MLMFDPVPVKQEAMDPV", "down_seq": "VSFPSNYIESMKPNKYGVIY", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser18", "evidence": [ { "id": "36852467", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36852467" }, { "id": "Q60980", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q60980" }, { "id": "40997131", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40997131" }, { "id": "34678516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34678516" }, { "id": "Q60980", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q60980" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "341", "end_pos": "341" } ] }, { "type": "snv", "site_list": [ { "start_pos": "290", "end_pos": "290" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q60980-1.10.10", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q60980-1.12.12", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q60980-1.10.10", "start_pos": 10, "end_pos": 10, "uniprot_canonical_ac": "Q60980-1", "length": 344, "uniprot_id": "KLF3_MOUSE", "protein_name": "Krueppel-like factor 3", "refseq_ac": "NP_032479", "refseq_name": "Krueppel-like factor 3", "gene_name": "Klf3", "gene_names_uniprotkb": "Klf3; Bklf", "gene_names_refseq": "9930027G08Rik; Bklf; Klf3; Tef-2", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Role for SUMO modification in facilitating transcriptional repression by BKLF.", "journal": "Molecular and cellular biology", "date": "2005", "authors": "Perdomo J, Verger A, Turner J, Crossley M", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "reference": [ { "type": "PubMed", "id": "15684403", "url": "https://glygen.org/publication/PubMed/15684403" } ] } ], "crossref": [ { "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15684403", "url": "https://glygen.org/publication/PubMed/15684403", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "MLMFDPVPV", "down_seq": "QEAMDPVSVSFPSNYIESMK", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "A", "comment": "Reduced sumoylation levels. No effect on DNA-binding and slight reduction of transcriptional repression. Abolishes sumoylation. No effect on DNA-binding but great reduction in transcriptional repression; when associated with A-197.", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "PubMed", "id": "15684403", "url": "https://glygen.org/publication/PubMed/15684403" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "341", "end_pos": "341" } ] }, { "type": "snv", "site_list": [ { "start_pos": "290", "end_pos": "290" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q60980-1.12.12", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q60980-1.18.18", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q60980-1.12.12", "start_pos": 12, "end_pos": 12, "uniprot_canonical_ac": "Q60980-1", "length": 344, "uniprot_id": "KLF3_MOUSE", "protein_name": "Krueppel-like factor 3", "refseq_ac": "NP_032479", "refseq_name": "Krueppel-like factor 3", "gene_name": "Klf3", "gene_names_uniprotkb": "Klf3; Bklf", "gene_names_refseq": "9930027G08Rik; Bklf; Klf3; Tef-2", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Role for SUMO modification in facilitating transcriptional repression by BKLF.", "journal": "Molecular and cellular biology", "date": "2005", "authors": "Perdomo J, Verger A, Turner J, Crossley M", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "reference": [ { "type": "PubMed", "id": "15684403", "url": "https://glygen.org/publication/PubMed/15684403" } ] } ], "crossref": [ { "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15684403", "url": "https://glygen.org/publication/PubMed/15684403", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "MLMFDPVPVKQ", "down_seq": "AMDPVSVSFPSNYIESMKPN", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "Slight reduction of transcriptional repression. Great reduction of transcriptional repression; when associated with A-199.", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "PubMed", "id": "15684403", "url": "https://glygen.org/publication/PubMed/15684403" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "341", "end_pos": "341" } ] }, { "type": "snv", "site_list": [ { "start_pos": "290", "end_pos": "290" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q60980-1.10.10", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q60980-1.18.18", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q60980-1.197.197", "start_pos": 197, "end_pos": 197, "uniprot_canonical_ac": "Q60980-1", "length": 344, "uniprot_id": "KLF3_MOUSE", "protein_name": "Krueppel-like factor 3", "refseq_ac": "NP_032479", "refseq_name": "Krueppel-like factor 3", "gene_name": "Klf3", "gene_names_uniprotkb": "Klf3; Bklf", "gene_names_refseq": "9930027G08Rik; Bklf; Klf3; Tef-2", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Role for SUMO modification in facilitating transcriptional repression by BKLF.", "journal": "Molecular and cellular biology", "date": "2005", "authors": "Perdomo J, Verger A, Turner J, Crossley M", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "reference": [ { "type": "PubMed", "id": "15684403", "url": "https://glygen.org/publication/PubMed/15684403" } ] } ], "crossref": [ { "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15684403", "url": "https://glygen.org/publication/PubMed/15684403", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SGMPVPVIESYEKPLLQKKI", "down_seq": "IEPGIEPQRTDYYPEEMSPP", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "A", "comment": "Reduced sumoylation levels. No effect on DNA-binding and slight reduction of transcriptional repression. Abolishes sumoylation. No effect on DNA-binding but great reduction of transcriptional repression; when associated with A-10.", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "PubMed", "id": "15684403", "url": "https://glygen.org/publication/PubMed/15684403" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "341", "end_pos": "341" } ] }, { "type": "snv", "site_list": [ { "start_pos": "290", "end_pos": "290" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q60980-1.199.199", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q60980-1.215.215", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q60980-1.199.199", "start_pos": 199, "end_pos": 199, "uniprot_canonical_ac": "Q60980-1", "length": 344, "uniprot_id": "KLF3_MOUSE", "protein_name": "Krueppel-like factor 3", "refseq_ac": "NP_032479", "refseq_name": "Krueppel-like factor 3", "gene_name": "Klf3", "gene_names_uniprotkb": "Klf3; Bklf", "gene_names_refseq": "9930027G08Rik; Bklf; Klf3; Tef-2", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Role for SUMO modification in facilitating transcriptional repression by BKLF.", "journal": "Molecular and cellular biology", "date": "2005", "authors": "Perdomo J, Verger A, Turner J, Crossley M", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "reference": [ { "type": "PubMed", "id": "15684403", "url": "https://glygen.org/publication/PubMed/15684403" } ] } ], "crossref": [ { "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "15684403", "url": "https://glygen.org/publication/PubMed/15684403", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "MPVPVIESYEKPLLQKKIKI", "down_seq": "PGIEPQRTDYYPEEMSPPLM", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "Slight reduction of transcriptional repression. Great reduction of transcriptional repression; when associated with A-199.", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "PubMed", "id": "15684403", "url": "https://glygen.org/publication/PubMed/15684403" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "341", "end_pos": "341" } ] }, { "type": "snv", "site_list": [ { "start_pos": "290", "end_pos": "290" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q60980-1.197.197", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q60980-1.215.215", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q60980-1.341.341", "start_pos": 341, "end_pos": 341, "uniprot_canonical_ac": "Q60980-1", "length": 344, "uniprot_id": "KLF3_MOUSE", "protein_name": "Krueppel-like factor 3", "refseq_ac": "NP_032479", "refseq_name": "Krueppel-like factor 3", "gene_name": "Klf3", "gene_names_uniprotkb": "Klf3; Bklf", "gene_names_refseq": "9930027G08Rik; Bklf; Klf3; Tef-2", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "CCHX zinc finger derivatives retain the ability to bind Zn(II) and mediate protein-DNA interactions.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Simpson RJ, Cram ED, Czolij R, Matthews JM, Crossley M, Mackay JP", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "reference": [ { "type": "PubMed", "id": "12736264", "url": "https://glygen.org/publication/PubMed/12736264" } ] } ], "crossref": [ { "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12736264", "url": "https://glygen.org/publication/PubMed/12736264", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "CPDCDRSFSRSDHLALHRKR", "down_seq": "MLV", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Little change in DNA-binding ability.", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "PubMed", "id": "12736264", "url": "https://glygen.org/publication/PubMed/12736264" } ] }, { "sequence_org": "H", "sequence_mut": "D", "comment": "Little change in DNA-binding ability.", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "PubMed", "id": "12736264", "url": "https://glygen.org/publication/PubMed/12736264" } ] }, { "sequence_org": "H", "sequence_mut": "E", "comment": "Little change in DNA-binding ability.", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "PubMed", "id": "12736264", "url": "https://glygen.org/publication/PubMed/12736264" } ] }, { "sequence_org": "H", "sequence_mut": "N", "comment": "Little change in DNA-binding ability.", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "PubMed", "id": "12736264", "url": "https://glygen.org/publication/PubMed/12736264" } ] }, { "sequence_org": "H", "sequence_mut": "Q", "comment": "Little change in DNA-binding ability.", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "PubMed", "id": "12736264", "url": "https://glygen.org/publication/PubMed/12736264" } ] }, { "sequence_org": "H", "sequence_mut": "R", "comment": "Little change in DNA-binding ability.", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "PubMed", "id": "12736264", "url": "https://glygen.org/publication/PubMed/12736264" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "341", "end_pos": "341" } ] }, { "type": "snv", "site_list": [ { "start_pos": "290", "end_pos": "290" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q60980-1.290.290", "start_pos": 290, "end_pos": 290, "uniprot_canonical_ac": "Q60980-1", "length": 344, "uniprot_id": "KLF3_MOUSE", "protein_name": "Krueppel-like factor 3", "refseq_ac": "NP_032479", "refseq_name": "Krueppel-like factor 3", "gene_name": "Klf3", "gene_names_uniprotkb": "Klf3; Bklf", "gene_names_refseq": "9930027G08Rik; Bklf; Klf3; Tef-2", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "rs3388747611", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3388747611", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "YTKSSHLKAHRRTHTGEKPY", "down_seq": "CTWEGCTWKFARSDELTRHF", "snv": [ { "evidence": [ { "id": "rs3388747611", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3388747611" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KCT->NCT).", "chr_id": "5", "chr_pos": "64986336", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K290", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "341", "end_pos": "341" } ] }, { "type": "snv", "site_list": [ { "start_pos": "290", "end_pos": "290" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q60980-1.100.100", "start_pos": 100, "end_pos": 100, "uniprot_canonical_ac": "Q60980-1", "length": 344, "uniprot_id": "KLF3_MOUSE", "protein_name": "Krueppel-like factor 3", "refseq_ac": "NP_032479", "refseq_name": "Krueppel-like factor 3", "gene_name": "Klf3", "gene_names_uniprotkb": "Klf3; Bklf", "gene_names_refseq": "9930027G08Rik; Bklf; Klf3; Tef-2", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "A tissue-specific atlas of mouse protein phosphorylation and expression.", "journal": "Cell", "date": "2010", "authors": "Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villen J, Haas W, Sowa ME, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "iPTMnet", "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980" } ], "reference": [ { "type": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" } ] } ], "crossref": [ { "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SSLKFPSHRRASPGLSMPSS", "down_seq": "PPIKKYSPPSPGVQPFGVPL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" }, { "database": "iPTMnet", "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980" } ], "site_lbl": "Ser100" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "341", "end_pos": "341" } ] }, { "type": "snv", "site_list": [ { "start_pos": "290", "end_pos": "290" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q60980-1.91.91", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q60980-1.107.107", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q60980-1.110.110", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q60980-1.107.107", "start_pos": 107, "end_pos": 107, "uniprot_canonical_ac": "Q60980-1", "length": 344, "uniprot_id": "KLF3_MOUSE", "protein_name": "Krueppel-like factor 3", "refseq_ac": "NP_032479", "refseq_name": "Krueppel-like factor 3", "gene_name": "Klf3", "gene_names_uniprotkb": "Klf3; Bklf", "gene_names_refseq": "9930027G08Rik; Bklf; Klf3; Tef-2", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "A tissue-specific atlas of mouse protein phosphorylation and expression.", "journal": "Cell", "date": "2010", "authors": "Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villen J, Haas W, Sowa ME, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "iPTMnet", "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980" } ], "reference": [ { "type": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" } ] } ], "crossref": [ { "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HRRASPGLSMPSSSPPIKKY", "down_seq": "PPSPGVQPFGVPLSMPPVMA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" }, { "database": "iPTMnet", "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980" } ], "site_lbl": "Ser107" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "341", "end_pos": "341" } ] }, { "type": "snv", "site_list": [ { "start_pos": "290", "end_pos": "290" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q60980-1.91.91", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q60980-1.100.100", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q60980-1.110.110", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q60980-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "Q60980-1", "length": 344, "uniprot_id": "KLF3_MOUSE", "protein_name": "Krueppel-like factor 3", "refseq_ac": "NP_032479", "refseq_name": "Krueppel-like factor 3", "gene_name": "Klf3", "gene_names_uniprotkb": "Klf3; Bklf", "gene_names_refseq": "9930027G08Rik; Bklf; Klf3; Tef-2", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "A tissue-specific atlas of mouse protein phosphorylation and expression.", "journal": "Cell", "date": "2010", "authors": "Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villen J, Haas W, Sowa ME, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "iPTMnet", "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980" } ], "reference": [ { "type": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" } ] } ], "crossref": [ { "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ASPGLSMPSSSPPIKKYSPP", "down_seq": "PGVQPFGVPLSMPPVMAAAL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" }, { "database": "iPTMnet", "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980" } ], "site_lbl": "Ser110" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "341", "end_pos": "341" } ] }, { "type": "snv", "site_list": [ { "start_pos": "290", "end_pos": "290" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q60980-1.91.91", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q60980-1.100.100", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q60980-1.107.107", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q60980-1.215.215", "start_pos": 215, "end_pos": 215, "uniprot_canonical_ac": "Q60980-1", "length": 344, "uniprot_id": "KLF3_MOUSE", "protein_name": "Krueppel-like factor 3", "refseq_ac": "NP_032479", "refseq_name": "Krueppel-like factor 3", "gene_name": "Klf3", "gene_names_uniprotkb": "Klf3; Bklf", "gene_names_refseq": "9930027G08Rik; Bklf; Klf3; Tef-2", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "A tissue-specific atlas of mouse protein phosphorylation and expression.", "journal": "Cell", "date": "2010", "authors": "Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villen J, Haas W, Sowa ME, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "iPTMnet", "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980" } ], "reference": [ { "type": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" } ] } ], "crossref": [ { "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KIKIEPGIEPQRTDYYPEEM", "down_seq": "PPLMNPVSPPQALLQENHPS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" }, { "database": "iPTMnet", "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980" } ], "site_lbl": "Ser215" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "341", "end_pos": "341" } ] }, { "type": "snv", "site_list": [ { "start_pos": "290", "end_pos": "290" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q60980-1.197.197", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q60980-1.199.199", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q60980-1.223.223", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q60980-1.223.223", "start_pos": 223, "end_pos": 223, "uniprot_canonical_ac": "Q60980-1", "length": 344, "uniprot_id": "KLF3_MOUSE", "protein_name": "Krueppel-like factor 3", "refseq_ac": "NP_032479", "refseq_name": "Krueppel-like factor 3", "gene_name": "Klf3", "gene_names_uniprotkb": "Klf3; Bklf", "gene_names_refseq": "9930027G08Rik; Bklf; Klf3; Tef-2", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "A tissue-specific atlas of mouse protein phosphorylation and expression.", "journal": "Cell", "date": "2010", "authors": "Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villen J, Haas W, Sowa ME, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "iPTMnet", "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980" } ], "reference": [ { "type": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" } ] } ], "crossref": [ { "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EPQRTDYYPEEMSPPLMNPV", "down_seq": "PPQALLQENHPSVIVQPGKR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" }, { "database": "iPTMnet", "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980" } ], "site_lbl": "Ser223" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "341", "end_pos": "341" } ] }, { "type": "snv", "site_list": [ { "start_pos": "290", "end_pos": "290" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q60980-1.215.215", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q60980-1.249.249", "start_pos": 249, "end_pos": 249, "uniprot_canonical_ac": "Q60980-1", "length": 344, "uniprot_id": "KLF3_MOUSE", "protein_name": "Krueppel-like factor 3", "refseq_ac": "NP_032479", "refseq_name": "Krueppel-like factor 3", "gene_name": "Klf3", "gene_names_uniprotkb": "Klf3; Bklf", "gene_names_refseq": "9930027G08Rik; Bklf; Klf3; Tef-2", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LQENHPSVIVQPGKRPLPVE", "down_seq": "PDTQRKRRIHRCDYDGCNKV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "site_lbl": "Ser249" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "341", "end_pos": "341" } ] }, { "type": "snv", "site_list": [ { "start_pos": "290", "end_pos": "290" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q60980-1.71.71", "start_pos": 71, "end_pos": 71, "uniprot_canonical_ac": "Q60980-1", "length": 344, "uniprot_id": "KLF3_MOUSE", "protein_name": "Krueppel-like factor 3", "refseq_ac": "NP_032479", "refseq_name": "Krueppel-like factor 3", "gene_name": "Klf3", "gene_names_uniprotkb": "Klf3; Bklf", "gene_names_refseq": "9930027G08Rik; Bklf; Klf3; Tef-2", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EGLTHGIQVEPVDLTVNKRG", "down_seq": "PPAAGGSPSSLKFPSHRRAS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "site_lbl": "Ser71" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "341", "end_pos": "341" } ] }, { "type": "snv", "site_list": [ { "start_pos": "290", "end_pos": "290" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "Q60980-1.91.91", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q60980-1.91.91", "start_pos": 91, "end_pos": 91, "uniprot_canonical_ac": "Q60980-1", "length": 344, "uniprot_id": "KLF3_MOUSE", "protein_name": "Krueppel-like factor 3", "refseq_ac": "NP_032479", "refseq_name": "Krueppel-like factor 3", "gene_name": "Klf3", "gene_names_uniprotkb": "Klf3; Bklf", "gene_names_refseq": "9930027G08Rik; Bklf; Klf3; Tef-2", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "A tissue-specific atlas of mouse protein phosphorylation and expression.", "journal": "Cell", "date": "2010", "authors": "Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villen J, Haas W, Sowa ME, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "iPTMnet", "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980" } ], "reference": [ { "type": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" } ] } ], "crossref": [ { "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPPAAGGSPSSLKFPSHRRA", "down_seq": "PGLSMPSSSPPIKKYSPPSP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q60980", "url": "https://www.uniprot.org/uniprotkb/Q60980" }, { "database": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" }, { "database": "iPTMnet", "id": "Q60980", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q60980" } ], "site_lbl": "Ser91" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "18", "end_pos": "18" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "199", "end_pos": "199" }, { "start_pos": "341", "end_pos": "341" } ] }, { "type": "snv", "site_list": [ { "start_pos": "290", "end_pos": "290" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "71", "end_pos": "71" }, { "start_pos": "91", "end_pos": "91" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q60980-1.71.71", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q60980-1.100.100", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q60980-1.107.107", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q60980-1.110.110", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P20444-1.657.657", "start_pos": 657, "end_pos": 657, "uniprot_canonical_ac": "P20444-1", "length": 672, "uniprot_id": "KPCA_MOUSE", "protein_name": "Protein kinase C alpha type", "refseq_ac": "NP_035231", "refseq_name": "protein kinase C alpha type", "gene_name": "Prkca", "gene_names_uniprotkb": "Prkca; Pkca", "gene_names_refseq": "Pkca; Prkca", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Essential function of TORC2 in PKC and Akt turn motif phosphorylation, maturation and signalling.", "journal": "The EMBO journal", "date": "2008-07-23", "authors": "Ikenoue Tsuneo, Inoki Ken, Yang Qian, Zhou Xiaoming, Guan Kun-Liang", "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "reference": [ { "type": "PubMed", "id": "18566587", "url": "https://glygen.org/publication/PubMed/18566587" } ] }, { "title": "A Ras activation pathway dependent on Syk phosphorylation of protein kinase C.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2003", "authors": "Kawakami Y, Kitaura J, Yao L, McHenry RW, Kawakami Y, Newton AC, Kang S, Kato RM, Leitges M, Rawlings DJ, Kawakami T", "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" }, { "database": "iPTMnet", "id": "P20444", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P20444" } ], "reference": [ { "type": "PubMed", "id": "12881490", "url": "https://glygen.org/publication/PubMed/12881490" } ] }, { "title": "Novel nootropic drug sunifiram enhances hippocampal synaptic efficacy via glycine-binding site of N-methyl-D-aspartate receptor.", "journal": "Hippocampus", "date": "2013", "authors": "Moriguchi S, Tanaka T, Narahashi T, Fukunaga K", "evidence": [ { "database": "iPTMnet", "id": "P20444", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P20444" } ], "reference": [ { "type": "PubMed", "id": "23733502", "url": "https://glygen.org/publication/PubMed/23733502" } ] }, { "title": "Anticonvulsant-like effect of thromboxane receptor agonist U-46619 against pentylenetetrazol-induced seizures.", "journal": "Epilepsy research", "date": "2018-10", "authors": "Freitas Mayara L\u00fctchemeyer de, Mello Fernanda Kulinski, Souza Tha\u00edze Lopes de, Grauncke Ana Claudia Beck, Fighera Michele Rechia, Royes Luiz Fernando Freire, Furian Ana Fl\u00e1via, Oliveira Mauro Schneider", "evidence": [ { "database": "iPTMnet", "id": "P20444", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P20444" } ], "reference": [ { "type": "PubMed", "id": "30153647", "url": "https://glygen.org/publication/PubMed/30153647" } ] } ], "crossref": [ { "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18566587", "url": "https://glygen.org/publication/PubMed/18566587", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P20444", "url": "https://www.ebi.ac.uk/intact/interactors/id:P20444*", "database": "IntAct", "categories": [ "Other" ] }, { "id": "P20444", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P20444", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "12881490", "url": "https://glygen.org/publication/PubMed/12881490", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23733502", "url": "https://glygen.org/publication/PubMed/23733502", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30153647", "url": "https://glygen.org/publication/PubMed/30153647", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LTPPDQLVIANIDQSDFEGF", "down_seq": "YVNPQFVHPILQSAV", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Abolished phosphorylation by mTORC2, leading to ubiquitinartion and degradation.", "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" }, { "database": "PubMed", "id": "18566587", "url": "https://glygen.org/publication/PubMed/18566587" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by MTOR", "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" }, { "database": "IntAct", "id": "P20444", "url": "https://www.ebi.ac.uk/intact/interactors/id:P20444*" }, { "database": "iPTMnet", "id": "P20444", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P20444" }, { "database": "PubMed", "id": "12881490", "url": "https://glygen.org/publication/PubMed/12881490" }, { "database": "PubMed", "id": "23733502", "url": "https://glygen.org/publication/PubMed/23733502" }, { "database": "PubMed", "id": "30153647", "url": "https://glygen.org/publication/PubMed/30153647" } ], "site_lbl": "Ser657" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "657", "end_pos": "657" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "658", "end_pos": "658" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P20444-1.638.638", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P20444-1.651.651", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P20444-1.658.658", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P20444-1.10.10", "start_pos": 10, "end_pos": 10, "uniprot_canonical_ac": "P20444-1", "length": 672, "uniprot_id": "KPCA_MOUSE", "protein_name": "Protein kinase C alpha type", "refseq_ac": "NP_035231", "refseq_name": "protein kinase C alpha type", "gene_name": "Prkca", "gene_names_uniprotkb": "Prkca; Pkca", "gene_names_refseq": "Pkca; Prkca", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MADVYPAND", "down_seq": "TASQDVANRFARKGALRQKN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "site_lbl": "Ser10" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "657", "end_pos": "657" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "658", "end_pos": "658" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P20444-1.226.226", "start_pos": 226, "end_pos": 226, "uniprot_canonical_ac": "P20444-1", "length": 672, "uniprot_id": "KPCA_MOUSE", "protein_name": "Protein kinase C alpha type", "refseq_ac": "NP_035231", "refseq_name": "protein kinase C alpha type", "gene_name": "Prkca", "gene_names_uniprotkb": "Prkca; Pkca", "gene_names_refseq": "Pkca; Prkca", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NESKQKTKTIRSNLNPQWNE", "down_seq": "FTFKLKPSDKDRRLSVEIWD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "site_lbl": "Ser226" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "657", "end_pos": "657" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "658", "end_pos": "658" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P20444-1.319.319", "start_pos": 319, "end_pos": 319, "uniprot_canonical_ac": "P20444-1", "length": 672, "uniprot_id": "KPCA_MOUSE", "protein_name": "Protein kinase C alpha type", "refseq_ac": "NP_035231", "refseq_name": "protein kinase C alpha type", "gene_name": "Prkca", "gene_names_uniprotkb": "Prkca; Pkca", "gene_names_refseq": "Pkca; Prkca", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MELRQKFEKAKLGPVGNKVI", "down_seq": "PSEDRKQPSNNLDRVKLTDF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "site_lbl": "Ser319" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "657", "end_pos": "657" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "658", "end_pos": "658" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P20444-1.494.494", "start_pos": 494, "end_pos": 494, "uniprot_canonical_ac": "P20444-1", "length": 672, "uniprot_id": "KPCA_MOUSE", "protein_name": "Protein kinase C alpha type", "refseq_ac": "NP_035231", "refseq_name": "protein kinase C alpha type", "gene_name": "Prkca", "gene_names_uniprotkb": "Prkca; Pkca", "gene_names_refseq": "Pkca; Prkca", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EGHIKIADFGMCKEHMMDGV", "down_seq": "TRTFCGTPDYIAPEIIAYQP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "site_lbl": "Thr494" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "657", "end_pos": "657" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "658", "end_pos": "658" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P20444-1.495.495", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P20444-1.497.497", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P20444-1.501.501", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P20444-1.495.495", "start_pos": 495, "end_pos": 495, "uniprot_canonical_ac": "P20444-1", "length": 672, "uniprot_id": "KPCA_MOUSE", "protein_name": "Protein kinase C alpha type", "refseq_ac": "NP_035231", "refseq_name": "protein kinase C alpha type", "gene_name": "Prkca", "gene_names_uniprotkb": "Prkca; Pkca", "gene_names_refseq": "Pkca; Prkca", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GHIKIADFGMCKEHMMDGVT", "down_seq": "RTFCGTPDYIAPEIIAYQPY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "site_lbl": "Thr495" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "657", "end_pos": "657" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "658", "end_pos": "658" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P20444-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P20444-1.497.497", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P20444-1.501.501", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P20444-1.497.497", "start_pos": 497, "end_pos": 497, "uniprot_canonical_ac": "P20444-1", "length": 672, "uniprot_id": "KPCA_MOUSE", "protein_name": "Protein kinase C alpha type", "refseq_ac": "NP_035231", "refseq_name": "protein kinase C alpha type", "gene_name": "Prkca", "gene_names_uniprotkb": "Prkca; Pkca", "gene_names_refseq": "Pkca; Prkca", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IKIADFGMCKEHMMDGVTTR", "down_seq": "FCGTPDYIAPEIIAYQPYGK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine; by PDPK1", "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "site_lbl": "Thr497" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "657", "end_pos": "657" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "658", "end_pos": "658" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P20444-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P20444-1.495.495", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P20444-1.501.501", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P20444-1.501.501", "start_pos": 501, "end_pos": 501, "uniprot_canonical_ac": "P20444-1", "length": 672, "uniprot_id": "KPCA_MOUSE", "protein_name": "Protein kinase C alpha type", "refseq_ac": "NP_035231", "refseq_name": "protein kinase C alpha type", "gene_name": "Prkca", "gene_names_uniprotkb": "Prkca; Pkca", "gene_names_refseq": "Pkca; Prkca", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DFGMCKEHMMDGVTTRTFCG", "down_seq": "PDYIAPEIIAYQPYGKSVDW", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "site_lbl": "Thr501" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "657", "end_pos": "657" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "658", "end_pos": "658" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P20444-1.494.494", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P20444-1.495.495", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P20444-1.497.497", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P20444-1.631.631", "start_pos": 631, "end_pos": 631, "uniprot_canonical_ac": "P20444-1", "length": 672, "uniprot_id": "KPCA_MOUSE", "protein_name": "Protein kinase C alpha type", "refseq_ac": "NP_035231", "refseq_name": "protein kinase C alpha type", "gene_name": "Prkca", "gene_names_uniprotkb": "Prkca; Pkca", "gene_names_refseq": "Pkca; Prkca", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QPPFKPKVCGKGAENFDKFF", "down_seq": "RGQPVLTPPDQLVIANIDQS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine; by MTOR", "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "site_lbl": "Thr631" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "657", "end_pos": "657" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "658", "end_pos": "658" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P20444-1.638.638", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P20444-1.651.651", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P20444-1.638.638", "start_pos": 638, "end_pos": 638, "uniprot_canonical_ac": "P20444-1", "length": 672, "uniprot_id": "KPCA_MOUSE", "protein_name": "Protein kinase C alpha type", "refseq_ac": "NP_035231", "refseq_name": "protein kinase C alpha type", "gene_name": "Prkca", "gene_names_uniprotkb": "Prkca; Pkca", "gene_names_refseq": "Pkca; Prkca", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Erk1/2-dependent phosphorylation of PKCalpha at threonine 638 in hippocampal 5-HT(1A) receptor-mediated signaling.", "journal": "Biochemical and biophysical research communications", "date": "2010", "authors": "Debata PR, Ranasinghe B, Berliner A, Curcio GM, Tantry SJ, Ponimaskin E, Banerjee P", "evidence": [ { "database": "iPTMnet", "id": "P20444", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P20444" } ], "reference": [ { "type": "PubMed", "id": "20513439", "url": "https://glygen.org/publication/PubMed/20513439" } ] } ], "crossref": [ { "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P20444", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P20444", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20513439", "url": "https://glygen.org/publication/PubMed/20513439", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VCGKGAENFDKFFTRGQPVL", "down_seq": "PPDQLVIANIDQSDFEGFSY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine; by autocatalysis", "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" }, { "database": "iPTMnet", "id": "P20444", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P20444" }, { "database": "PubMed", "id": "20513439", "url": "https://glygen.org/publication/PubMed/20513439" } ], "site_lbl": "Thr638" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "657", "end_pos": "657" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "658", "end_pos": "658" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P20444-1.631.631", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P20444-1.651.651", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P20444-1.657.657", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P20444-1.658.658", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P20444-1.651.651", "start_pos": 651, "end_pos": 651, "uniprot_canonical_ac": "P20444-1", "length": 672, "uniprot_id": "KPCA_MOUSE", "protein_name": "Protein kinase C alpha type", "refseq_ac": "NP_035231", "refseq_name": "protein kinase C alpha type", "gene_name": "Prkca", "gene_names_uniprotkb": "Prkca; Pkca", "gene_names_refseq": "Pkca; Prkca", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TRGQPVLTPPDQLVIANIDQ", "down_seq": "DFEGFSYVNPQFVHPILQSA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "site_lbl": "Ser651" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "657", "end_pos": "657" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "658", "end_pos": "658" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P20444-1.631.631", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P20444-1.638.638", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P20444-1.657.657", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P20444-1.658.658", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P20444-1.658.658", "start_pos": 658, "end_pos": 658, "uniprot_canonical_ac": "P20444-1", "length": 672, "uniprot_id": "KPCA_MOUSE", "protein_name": "Protein kinase C alpha type", "refseq_ac": "NP_035231", "refseq_name": "protein kinase C alpha type", "gene_name": "Prkca", "gene_names_uniprotkb": "Prkca; Pkca", "gene_names_refseq": "Pkca; Prkca", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "A Ras activation pathway dependent on Syk phosphorylation of protein kinase C.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2003", "authors": "Kawakami Y, Kitaura J, Yao L, McHenry RW, Kawakami Y, Newton AC, Kang S, Kato RM, Leitges M, Rawlings DJ, Kawakami T", "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" }, { "database": "iPTMnet", "id": "P20444", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P20444" } ], "reference": [ { "type": "PubMed", "id": "12881490", "url": "https://glygen.org/publication/PubMed/12881490" } ] } ], "crossref": [ { "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P20444", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P20444", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "12881490", "url": "https://glygen.org/publication/PubMed/12881490", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "TPPDQLVIANIDQSDFEGFS", "down_seq": "VNPQFVHPILQSAV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine; by SYK", "evidence": [ { "database": "UniProtKB", "id": "P20444", "url": "https://www.uniprot.org/uniprotkb/P20444" }, { "database": "iPTMnet", "id": "P20444", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P20444" }, { "database": "PubMed", "id": "12881490", "url": "https://glygen.org/publication/PubMed/12881490" } ], "site_lbl": "Tyr658" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "657", "end_pos": "657" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "10", "end_pos": "10" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "495", "end_pos": "495" }, { "start_pos": "497", "end_pos": "497" }, { "start_pos": "501", "end_pos": "501" }, { "start_pos": "631", "end_pos": "631" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "657", "end_pos": "657" }, { "start_pos": "658", "end_pos": "658" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P20444-1.638.638", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P20444-1.651.651", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P20444-1.657.657", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6ZPY7-1.1283.1283", "start_pos": 1283, "end_pos": 1283, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "GLY_001153", "url": "https://data.glygen.org/GLY_001153", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "STAKVSPLTPKLFNSLLLGP", "down_seq": "ASNSKTEGSSLRDLLHSGPG", "glycosylation": [ { "glytoucan_ac": "", "type": "O-linked", "subtype": "", "prediction_tool_list": [ { "label": "isoglyp", "url": "https://github.com/jonmohl/ISOGlyP" } ], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr1283", "evidence": [ { "id": "GLY_001153", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001153" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q6ZPY7-1.1266.1266", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZPY7-1.388.388", "start_pos": 388, "end_pos": 388, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "O-GlcNAcylation Is Essential for Rapid Pomc Expression and Cell Proliferation in Corticotropic Tumor Cells.", "journal": "Endocrinology", "date": "2021", "authors": "Massman LJ, Pereckas M, Zwagerman NT, Olivier-Van Stichelen S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053" } ] }, { "title": "Chemoproteomic and Transcriptomic Analysis Reveals that O-GlcNAc Regulates Mouse Embryonic Stem Cell Fate through the Pluripotency Network.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2023-02-27", "authors": "Hao Yi, Li Xiang, Qin Ke, Shi Yujie, He Yanwen, Zhang Che, Cheng Bo, Zhang Xiwen, Hu Guangyu, Liang Shuyu, Tang Qi, Chen Xing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467" } ] }, { "title": "Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316" } ] }, { "title": "Dynamic O-GlcNAcylation governs long-range chromatin interactions in V(D)J recombination during early B-cell development.", "journal": "Cellular & molecular immunology", "date": "2025-01", "authors": "Jeon Bong Chan, Kim Yu-Ji, Park Ae Kyung, Song Mi-Ran, Na Ki Myeong, Lee Juwon, An Dasom, Park Yeseul, Hwang Heeyoun, Kim Tae-Don, Lim Junghyun, Park Sung-Kyun", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609" } ] }, { "title": "Comprehensive Evaluation of Cleavable Bioorthogonal Probes for Site-Specific O-GlcNAc Proteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2025-10", "authors": "Hou Chunyan, Zhang Hemeng, Deng Jingtao, Wang Xiaoxin, Byers Stephen, Levi Moshe, Pak Daniel T S, Moremen Kelley W, Pei Huadong, Hart Gerald W, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482" } ] }, { "title": "Polycomb repressive complex 2 is necessary for the normal site-specific O-GlcNAc distribution in mouse embryonic stem cells.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Myers SA, Panning B, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "crossref": [ { "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LVVQDEPVGGDTPVPFTPYA", "down_seq": "ATGQTPLAPEVGGAENKEAG", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser388", "evidence": [ { "id": "34418053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34418053" }, { "id": "Q6ZPY7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" }, { "id": "36852467", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36852467" }, { "id": "22645316", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22645316" }, { "id": "39627609", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39627609" }, { "id": "40885482", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40885482" }, { "id": "21606357", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6ZPY7-1.410.410", "start_pos": 410, "end_pos": 410, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "O-GlcNAcylation Is Essential for Rapid Pomc Expression and Cell Proliferation in Corticotropic Tumor Cells.", "journal": "Endocrinology", "date": "2021", "authors": "Massman LJ, Pereckas M, Zwagerman NT, Olivier-Van Stichelen S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053" } ] }, { "title": "Chemoproteomic and Transcriptomic Analysis Reveals that O-GlcNAc Regulates Mouse Embryonic Stem Cell Fate through the Pluripotency Network.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2023-02-27", "authors": "Hao Yi, Li Xiang, Qin Ke, Shi Yujie, He Yanwen, Zhang Che, Cheng Bo, Zhang Xiwen, Hu Guangyu, Liang Shuyu, Tang Qi, Chen Xing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467" } ] }, { "title": "Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316" } ] }, { "title": "Dynamic O-GlcNAcylation governs long-range chromatin interactions in V(D)J recombination during early B-cell development.", "journal": "Cellular & molecular immunology", "date": "2025-01", "authors": "Jeon Bong Chan, Kim Yu-Ji, Park Ae Kyung, Song Mi-Ran, Na Ki Myeong, Lee Juwon, An Dasom, Park Yeseul, Hwang Heeyoun, Kim Tae-Don, Lim Junghyun, Park Sung-Kyun", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609" } ] }, { "title": "Comprehensive Evaluation of Cleavable Bioorthogonal Probes for Site-Specific O-GlcNAc Proteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2025-10", "authors": "Hou Chunyan, Zhang Hemeng, Deng Jingtao, Wang Xiaoxin, Byers Stephen, Levi Moshe, Pak Daniel T S, Moremen Kelley W, Pei Huadong, Hart Gerald W, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482" } ] }, { "title": "Polycomb repressive complex 2 is necessary for the normal site-specific O-GlcNAc distribution in mouse embryonic stem cells.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Myers SA, Panning B, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "crossref": [ { "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TGQTPLAPEVGGAENKEAGK", "down_seq": "LEQVSQGMVASAAVVTTASS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr410", "evidence": [ { "id": "34418053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34418053" }, { "id": "Q6ZPY7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" }, { "id": "36852467", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36852467" }, { "id": "22645316", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22645316" }, { "id": "39627609", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39627609" }, { "id": "40885482", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40885482" }, { "id": "21606357", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q6ZPY7-1.415.415", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6ZPY7-1.421.421", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q6ZPY7-1.426.426", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6ZPY7-1.427.427", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6ZPY7-1.415.415", "start_pos": 415, "end_pos": 415, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "O-GlcNAcylation Is Essential for Rapid Pomc Expression and Cell Proliferation in Corticotropic Tumor Cells.", "journal": "Endocrinology", "date": "2021", "authors": "Massman LJ, Pereckas M, Zwagerman NT, Olivier-Van Stichelen S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053" } ] }, { "title": "Chemoproteomic and Transcriptomic Analysis Reveals that O-GlcNAc Regulates Mouse Embryonic Stem Cell Fate through the Pluripotency Network.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2023-02-27", "authors": "Hao Yi, Li Xiang, Qin Ke, Shi Yujie, He Yanwen, Zhang Che, Cheng Bo, Zhang Xiwen, Hu Guangyu, Liang Shuyu, Tang Qi, Chen Xing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467" } ] }, { "title": "Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316" } ] }, { "title": "Dynamic O-GlcNAcylation governs long-range chromatin interactions in V(D)J recombination during early B-cell development.", "journal": "Cellular & molecular immunology", "date": "2025-01", "authors": "Jeon Bong Chan, Kim Yu-Ji, Park Ae Kyung, Song Mi-Ran, Na Ki Myeong, Lee Juwon, An Dasom, Park Yeseul, Hwang Heeyoun, Kim Tae-Don, Lim Junghyun, Park Sung-Kyun", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609" } ] }, { "title": "Comprehensive Evaluation of Cleavable Bioorthogonal Probes for Site-Specific O-GlcNAc Proteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2025-10", "authors": "Hou Chunyan, Zhang Hemeng, Deng Jingtao, Wang Xiaoxin, Byers Stephen, Levi Moshe, Pak Daniel T S, Moremen Kelley W, Pei Huadong, Hart Gerald W, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482" } ] }, { "title": "Polycomb repressive complex 2 is necessary for the normal site-specific O-GlcNAc distribution in mouse embryonic stem cells.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Myers SA, Panning B, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "crossref": [ { "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LAPEVGGAENKEAGKTLEQV", "down_seq": "QGMVASAAVVTTASSTPTTV", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser415", "evidence": [ { "id": "34418053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34418053" }, { "id": "Q6ZPY7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" }, { "id": "36852467", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36852467" }, { "id": "22645316", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22645316" }, { "id": "39627609", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39627609" }, { "id": "40885482", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40885482" }, { "id": "21606357", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q6ZPY7-1.410.410", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6ZPY7-1.421.421", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6ZPY7-1.426.426", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q6ZPY7-1.427.427", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6ZPY7-1.421.421", "start_pos": 421, "end_pos": 421, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "O-GlcNAcylation Is Essential for Rapid Pomc Expression and Cell Proliferation in Corticotropic Tumor Cells.", "journal": "Endocrinology", "date": "2021", "authors": "Massman LJ, Pereckas M, Zwagerman NT, Olivier-Van Stichelen S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053" } ] }, { "title": "Chemoproteomic and Transcriptomic Analysis Reveals that O-GlcNAc Regulates Mouse Embryonic Stem Cell Fate through the Pluripotency Network.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2023-02-27", "authors": "Hao Yi, Li Xiang, Qin Ke, Shi Yujie, He Yanwen, Zhang Che, Cheng Bo, Zhang Xiwen, Hu Guangyu, Liang Shuyu, Tang Qi, Chen Xing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467" } ] }, { "title": "Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316" } ] }, { "title": "Dynamic O-GlcNAcylation governs long-range chromatin interactions in V(D)J recombination during early B-cell development.", "journal": "Cellular & molecular immunology", "date": "2025-01", "authors": "Jeon Bong Chan, Kim Yu-Ji, Park Ae Kyung, Song Mi-Ran, Na Ki Myeong, Lee Juwon, An Dasom, Park Yeseul, Hwang Heeyoun, Kim Tae-Don, Lim Junghyun, Park Sung-Kyun", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609" } ] }, { "title": "Comprehensive Evaluation of Cleavable Bioorthogonal Probes for Site-Specific O-GlcNAc Proteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2025-10", "authors": "Hou Chunyan, Zhang Hemeng, Deng Jingtao, Wang Xiaoxin, Byers Stephen, Levi Moshe, Pak Daniel T S, Moremen Kelley W, Pei Huadong, Hart Gerald W, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482" } ] }, { "title": "Polycomb repressive complex 2 is necessary for the normal site-specific O-GlcNAc distribution in mouse embryonic stem cells.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Myers SA, Panning B, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "crossref": [ { "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GAENKEAGKTLEQVSQGMVA", "down_seq": "AAVVTTASSTPTTVRISDTG", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser421", "evidence": [ { "id": "34418053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34418053" }, { "id": "Q6ZPY7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" }, { "id": "36852467", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36852467" }, { "id": "22645316", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22645316" }, { "id": "39627609", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39627609" }, { "id": "40885482", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40885482" }, { "id": "21606357", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q6ZPY7-1.410.410", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6ZPY7-1.415.415", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q6ZPY7-1.426.426", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6ZPY7-1.427.427", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6ZPY7-1.426.426", "start_pos": 426, "end_pos": 426, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "O-GlcNAcylation Is Essential for Rapid Pomc Expression and Cell Proliferation in Corticotropic Tumor Cells.", "journal": "Endocrinology", "date": "2021", "authors": "Massman LJ, Pereckas M, Zwagerman NT, Olivier-Van Stichelen S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053" } ] }, { "title": "Chemoproteomic and Transcriptomic Analysis Reveals that O-GlcNAc Regulates Mouse Embryonic Stem Cell Fate through the Pluripotency Network.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2023-02-27", "authors": "Hao Yi, Li Xiang, Qin Ke, Shi Yujie, He Yanwen, Zhang Che, Cheng Bo, Zhang Xiwen, Hu Guangyu, Liang Shuyu, Tang Qi, Chen Xing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467" } ] }, { "title": "Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316" } ] }, { "title": "Dynamic O-GlcNAcylation governs long-range chromatin interactions in V(D)J recombination during early B-cell development.", "journal": "Cellular & molecular immunology", "date": "2025-01", "authors": "Jeon Bong Chan, Kim Yu-Ji, Park Ae Kyung, Song Mi-Ran, Na Ki Myeong, Lee Juwon, An Dasom, Park Yeseul, Hwang Heeyoun, Kim Tae-Don, Lim Junghyun, Park Sung-Kyun", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609" } ] }, { "title": "Comprehensive Evaluation of Cleavable Bioorthogonal Probes for Site-Specific O-GlcNAc Proteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2025-10", "authors": "Hou Chunyan, Zhang Hemeng, Deng Jingtao, Wang Xiaoxin, Byers Stephen, Levi Moshe, Pak Daniel T S, Moremen Kelley W, Pei Huadong, Hart Gerald W, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482" } ] }, { "title": "Polycomb repressive complex 2 is necessary for the normal site-specific O-GlcNAc distribution in mouse embryonic stem cells.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Myers SA, Panning B, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "crossref": [ { "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EAGKTLEQVSQGMVASAAVV", "down_seq": "TASSTPTTVRISDTGLASGT", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr426", "evidence": [ { "id": "34418053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34418053" }, { "id": "Q6ZPY7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" }, { "id": "36852467", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36852467" }, { "id": "22645316", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22645316" }, { "id": "39627609", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39627609" }, { "id": "40885482", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40885482" }, { "id": "21606357", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q6ZPY7-1.410.410", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q6ZPY7-1.415.415", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q6ZPY7-1.421.421", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q6ZPY7-1.427.427", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6ZPY7-1.427.427", "start_pos": 427, "end_pos": 427, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "O-GlcNAcylation Is Essential for Rapid Pomc Expression and Cell Proliferation in Corticotropic Tumor Cells.", "journal": "Endocrinology", "date": "2021", "authors": "Massman LJ, Pereckas M, Zwagerman NT, Olivier-Van Stichelen S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053" } ] }, { "title": "Chemoproteomic and Transcriptomic Analysis Reveals that O-GlcNAc Regulates Mouse Embryonic Stem Cell Fate through the Pluripotency Network.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2023-02-27", "authors": "Hao Yi, Li Xiang, Qin Ke, Shi Yujie, He Yanwen, Zhang Che, Cheng Bo, Zhang Xiwen, Hu Guangyu, Liang Shuyu, Tang Qi, Chen Xing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467" } ] }, { "title": "Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316" } ] }, { "title": "Dynamic O-GlcNAcylation governs long-range chromatin interactions in V(D)J recombination during early B-cell development.", "journal": "Cellular & molecular immunology", "date": "2025-01", "authors": "Jeon Bong Chan, Kim Yu-Ji, Park Ae Kyung, Song Mi-Ran, Na Ki Myeong, Lee Juwon, An Dasom, Park Yeseul, Hwang Heeyoun, Kim Tae-Don, Lim Junghyun, Park Sung-Kyun", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609" } ] }, { "title": "Comprehensive Evaluation of Cleavable Bioorthogonal Probes for Site-Specific O-GlcNAc Proteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2025-10", "authors": "Hou Chunyan, Zhang Hemeng, Deng Jingtao, Wang Xiaoxin, Byers Stephen, Levi Moshe, Pak Daniel T S, Moremen Kelley W, Pei Huadong, Hart Gerald W, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482" } ] }, { "title": "Polycomb repressive complex 2 is necessary for the normal site-specific O-GlcNAc distribution in mouse embryonic stem cells.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Myers SA, Panning B, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "crossref": [ { "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AGKTLEQVSQGMVASAAVVT", "down_seq": "ASSTPTTVRISDTGLASGTG", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "T", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr427", "evidence": [ { "id": "34418053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34418053" }, { "id": "Q6ZPY7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" }, { "id": "36852467", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36852467" }, { "id": "22645316", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22645316" }, { "id": "39627609", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39627609" }, { "id": "40885482", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40885482" }, { "id": "21606357", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q6ZPY7-1.410.410", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q6ZPY7-1.415.415", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6ZPY7-1.421.421", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q6ZPY7-1.426.426", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6ZPY7-1.655.655", "start_pos": 655, "end_pos": 655, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "O-GlcNAcylation Is Essential for Rapid Pomc Expression and Cell Proliferation in Corticotropic Tumor Cells.", "journal": "Endocrinology", "date": "2021", "authors": "Massman LJ, Pereckas M, Zwagerman NT, Olivier-Van Stichelen S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053" } ] }, { "title": "Chemoproteomic and Transcriptomic Analysis Reveals that O-GlcNAc Regulates Mouse Embryonic Stem Cell Fate through the Pluripotency Network.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2023-02-27", "authors": "Hao Yi, Li Xiang, Qin Ke, Shi Yujie, He Yanwen, Zhang Che, Cheng Bo, Zhang Xiwen, Hu Guangyu, Liang Shuyu, Tang Qi, Chen Xing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467" } ] }, { "title": "Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316" } ] }, { "title": "Dynamic O-GlcNAcylation governs long-range chromatin interactions in V(D)J recombination during early B-cell development.", "journal": "Cellular & molecular immunology", "date": "2025-01", "authors": "Jeon Bong Chan, Kim Yu-Ji, Park Ae Kyung, Song Mi-Ran, Na Ki Myeong, Lee Juwon, An Dasom, Park Yeseul, Hwang Heeyoun, Kim Tae-Don, Lim Junghyun, Park Sung-Kyun", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609" } ] }, { "title": "Comprehensive Evaluation of Cleavable Bioorthogonal Probes for Site-Specific O-GlcNAc Proteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2025-10", "authors": "Hou Chunyan, Zhang Hemeng, Deng Jingtao, Wang Xiaoxin, Byers Stephen, Levi Moshe, Pak Daniel T S, Moremen Kelley W, Pei Huadong, Hart Gerald W, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482" } ] }, { "title": "Polycomb repressive complex 2 is necessary for the normal site-specific O-GlcNAc distribution in mouse embryonic stem cells.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Myers SA, Panning B, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "crossref": [ { "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs3389502454", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3389502454", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SNPFLAFVEKVEHSPFSSFV", "down_seq": "QASGSSSSATSVTSKATASW", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser655", "evidence": [ { "id": "34418053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34418053" }, { "id": "Q6ZPY7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" }, { "id": "36852467", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36852467" }, { "id": "22645316", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22645316" }, { "id": "39627609", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39627609" }, { "id": "40885482", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40885482" }, { "id": "21606357", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "snv": [ { "evidence": [ { "id": "rs3389502454", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3389502454" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->F).", "chr_id": "18", "chr_pos": "34941874", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S655", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q6ZPY7-1.658.658", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6ZPY7-1.661.661", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6ZPY7-1.658.658", "start_pos": 658, "end_pos": 658, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "O-GlcNAcylation Is Essential for Rapid Pomc Expression and Cell Proliferation in Corticotropic Tumor Cells.", "journal": "Endocrinology", "date": "2021", "authors": "Massman LJ, Pereckas M, Zwagerman NT, Olivier-Van Stichelen S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053" } ] }, { "title": "Chemoproteomic and Transcriptomic Analysis Reveals that O-GlcNAc Regulates Mouse Embryonic Stem Cell Fate through the Pluripotency Network.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2023-02-27", "authors": "Hao Yi, Li Xiang, Qin Ke, Shi Yujie, He Yanwen, Zhang Che, Cheng Bo, Zhang Xiwen, Hu Guangyu, Liang Shuyu, Tang Qi, Chen Xing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467" } ] }, { "title": "Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316" } ] }, { "title": "Dynamic O-GlcNAcylation governs long-range chromatin interactions in V(D)J recombination during early B-cell development.", "journal": "Cellular & molecular immunology", "date": "2025-01", "authors": "Jeon Bong Chan, Kim Yu-Ji, Park Ae Kyung, Song Mi-Ran, Na Ki Myeong, Lee Juwon, An Dasom, Park Yeseul, Hwang Heeyoun, Kim Tae-Don, Lim Junghyun, Park Sung-Kyun", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609" } ] }, { "title": "Comprehensive Evaluation of Cleavable Bioorthogonal Probes for Site-Specific O-GlcNAc Proteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2025-10", "authors": "Hou Chunyan, Zhang Hemeng, Deng Jingtao, Wang Xiaoxin, Byers Stephen, Levi Moshe, Pak Daniel T S, Moremen Kelley W, Pei Huadong, Hart Gerald W, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482" } ] }, { "title": "Polycomb repressive complex 2 is necessary for the normal site-specific O-GlcNAc distribution in mouse embryonic stem cells.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Myers SA, Panning B, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "crossref": [ { "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FLAFVEKVEHSPFSSFVSQA", "down_seq": "GSSSSATSVTSKATASWPES", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser658", "evidence": [ { "id": "34418053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34418053" }, { "id": "Q6ZPY7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" }, { "id": "36852467", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36852467" }, { "id": "22645316", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22645316" }, { "id": "39627609", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39627609" }, { "id": "40885482", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40885482" }, { "id": "21606357", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q6ZPY7-1.655.655", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q6ZPY7-1.661.661", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6ZPY7-1.661.661", "start_pos": 661, "end_pos": 661, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "O-GlcNAcylation Is Essential for Rapid Pomc Expression and Cell Proliferation in Corticotropic Tumor Cells.", "journal": "Endocrinology", "date": "2021", "authors": "Massman LJ, Pereckas M, Zwagerman NT, Olivier-Van Stichelen S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053" } ] }, { "title": "Chemoproteomic and Transcriptomic Analysis Reveals that O-GlcNAc Regulates Mouse Embryonic Stem Cell Fate through the Pluripotency Network.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2023-02-27", "authors": "Hao Yi, Li Xiang, Qin Ke, Shi Yujie, He Yanwen, Zhang Che, Cheng Bo, Zhang Xiwen, Hu Guangyu, Liang Shuyu, Tang Qi, Chen Xing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467" } ] }, { "title": "Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316" } ] }, { "title": "Dynamic O-GlcNAcylation governs long-range chromatin interactions in V(D)J recombination during early B-cell development.", "journal": "Cellular & molecular immunology", "date": "2025-01", "authors": "Jeon Bong Chan, Kim Yu-Ji, Park Ae Kyung, Song Mi-Ran, Na Ki Myeong, Lee Juwon, An Dasom, Park Yeseul, Hwang Heeyoun, Kim Tae-Don, Lim Junghyun, Park Sung-Kyun", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609" } ] }, { "title": "Comprehensive Evaluation of Cleavable Bioorthogonal Probes for Site-Specific O-GlcNAc Proteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2025-10", "authors": "Hou Chunyan, Zhang Hemeng, Deng Jingtao, Wang Xiaoxin, Byers Stephen, Levi Moshe, Pak Daniel T S, Moremen Kelley W, Pei Huadong, Hart Gerald W, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482" } ] }, { "title": "Polycomb repressive complex 2 is necessary for the normal site-specific O-GlcNAc distribution in mouse embryonic stem cells.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Myers SA, Panning B, Burlingame AL", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "crossref": [ { "id": "34418053", "url": "https://glygen.org/publication/PubMed/34418053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZPY7", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "36852467", "url": "https://glygen.org/publication/PubMed/36852467", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22645316", "url": "https://glygen.org/publication/PubMed/22645316", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39627609", "url": "https://glygen.org/publication/PubMed/39627609", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40885482", "url": "https://glygen.org/publication/PubMed/40885482", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21606357", "url": "https://glygen.org/publication/PubMed/21606357", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FVEKVEHSPFSSFVSQASGS", "down_seq": "SSATSVTSKATASWPESHSS", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser661", "evidence": [ { "id": "34418053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34418053" }, { "id": "Q6ZPY7", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZPY7" }, { "id": "36852467", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/36852467" }, { "id": "22645316", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22645316" }, { "id": "39627609", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39627609" }, { "id": "40885482", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40885482" }, { "id": "21606357", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21606357" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q6ZPY7-1.655.655", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q6ZPY7-1.658.658", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6ZPY7-1.1266.1266", "start_pos": 1266, "end_pos": 1266, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "rs3389489080", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3389489080", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SVLNKESHSPFGLDSFNSTA", "down_seq": "VSPLTPKLFNSLLLGPTASN", "snv": [ { "evidence": [ { "id": "rs3389489080", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3389489080" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KVS->NVS).", "chr_id": "18", "chr_pos": "34957834", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1266", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q6ZPY7-1.1254.1254", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6ZPY7-1.1260.1260", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6ZPY7-1.1283.1283", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZPY7-1.1571.1571", "start_pos": 1571, "end_pos": 1571, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "rs3389494472", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3389494472", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "EDRRVGTTNLHLDVSDAVNV", "down_seq": "VYVGIPVGEGAHDEEVLKTI", "snv": [ { "evidence": [ { "id": "rs3389494472", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3389494472" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVM->NVT).", "chr_id": "18", "chr_pos": "34963257", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M1571", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZPY7-1.269.269", "start_pos": 269, "end_pos": 269, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "rs3389505052", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3389505052", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "HVMLMDSSTPQSEGGTIKAV", "down_seq": "SSKGKKKRESIEGRDGRRRK", "snv": [ { "evidence": [ { "id": "rs3389505052", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3389505052" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KSS->NSS).", "chr_id": "18", "chr_pos": "34936526", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K269", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZPY7-1.509.509", "start_pos": 509, "end_pos": 509, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "rs3389403544", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3389403544", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GRSQSNGVLATDNKPLGFSF", "down_seq": "CSSASESQKDSDLSKNLFFQ", "snv": [ { "evidence": [ { "id": "rs3389403544", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3389403544" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SCS->NCS).", "chr_id": "18", "chr_pos": "34941436", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S509", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q6ZPY7-1.493.493", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZPY7-1.1254.1254", "start_pos": 1254, "end_pos": 1254, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AKEETKDAGSLRSVLNKESH", "down_seq": "PFGLDSFNSTAKVSPLTPKL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "site_lbl": "Ser1254" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q6ZPY7-1.1260.1260", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q6ZPY7-1.1266.1266", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZPY7-1.1260.1260", "start_pos": 1260, "end_pos": 1260, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DAGSLRSVLNKESHSPFGLD", "down_seq": "FNSTAKVSPLTPKLFNSLLL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "site_lbl": "Ser1260" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q6ZPY7-1.1254.1254", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6ZPY7-1.1266.1266", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZPY7-1.493.493", "start_pos": 493, "end_pos": 493, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FGVSLSSLSQPLTFGSGRSQ", "down_seq": "NGVLATDNKPLGFSFSCSSA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "site_lbl": "Ser493" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q6ZPY7-1.509.509", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZPY7-1.547.547", "start_pos": 547, "end_pos": 547, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "A tissue-specific atlas of mouse protein phosphorylation and expression.", "journal": "Cell", "date": "2010", "authors": "Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villen J, Haas W, Sowa ME, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" }, { "database": "iPTMnet", "id": "Q6ZPY7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" } ] } ], "crossref": [ { "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZPY7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZPY7", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FFQCMSQNVPSTNYLSRVSE", "down_seq": "VADDSSSRDSFTQSLESLTS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" }, { "database": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" }, { "database": "iPTMnet", "id": "Q6ZPY7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZPY7" } ], "site_lbl": "Ser547" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q6ZPY7-1.557.557", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6ZPY7-1.561.561", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6ZPY7-1.557.557", "start_pos": 557, "end_pos": 557, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "A tissue-specific atlas of mouse protein phosphorylation and expression.", "journal": "Cell", "date": "2010", "authors": "Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villen J, Haas W, Sowa ME, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" }, { "database": "iPTMnet", "id": "Q6ZPY7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" } ] } ], "crossref": [ { "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZPY7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZPY7", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STNYLSRVSESVADDSSSRD", "down_seq": "FTQSLESLTSGLCKGRSVLG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" }, { "database": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" }, { "database": "iPTMnet", "id": "Q6ZPY7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZPY7" } ], "site_lbl": "Ser557" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q6ZPY7-1.547.547", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6ZPY7-1.561.561", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6ZPY7-1.561.561", "start_pos": 561, "end_pos": 561, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "A tissue-specific atlas of mouse protein phosphorylation and expression.", "journal": "Cell", "date": "2010", "authors": "Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villen J, Haas W, Sowa ME, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" }, { "database": "iPTMnet", "id": "Q6ZPY7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZPY7" } ], "reference": [ { "type": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" } ] } ], "crossref": [ { "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZPY7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZPY7", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LSRVSESVADDSSSRDSFTQ", "down_seq": "LESLTSGLCKGRSVLGADTQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" }, { "database": "PubMed", "id": "21183079", "url": "https://glygen.org/publication/PubMed/21183079" }, { "database": "iPTMnet", "id": "Q6ZPY7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZPY7" } ], "site_lbl": "Ser561" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6ZPY7-1.547.547", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6ZPY7-1.557.557", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6ZPY7-1.615.615", "start_pos": 615, "end_pos": 615, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PAESMPTLTPAFPRSLLNTR", "down_seq": "PENHENLFLQPPKLSREEPS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "site_lbl": "Thr615" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZPY7-1.767.767", "start_pos": 767, "end_pos": 767, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TEERPTVGPGQQDNPLLKTF", "down_seq": "TVFGRHSGSFLSAPAEFAQE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "site_lbl": "Ser767" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q6ZPY7-1.774.774", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q6ZPY7-1.779.779", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZPY7-1.774.774", "start_pos": 774, "end_pos": 774, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GPGQQDNPLLKTFSTVFGRH", "down_seq": "GSFLSAPAEFAQENKAPFEA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "site_lbl": "Ser774" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q6ZPY7-1.767.767", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q6ZPY7-1.779.779", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZPY7-1.779.779", "start_pos": 779, "end_pos": 779, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DNPLLKTFSTVFGRHSGSFL", "down_seq": "APAEFAQENKAPFEAVKRFS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "site_lbl": "Ser779" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q6ZPY7-1.767.767", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q6ZPY7-1.774.774", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q6ZPY7-1.799.799", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZPY7-1.799.799", "start_pos": 799, "end_pos": 799, "uniprot_canonical_ac": "Q6ZPY7-1", "length": 1762, "uniprot_id": "KDM3B_MOUSE", "protein_name": "Lysine-specific demethylase 3B", "refseq_ac": "NP_001074725", "refseq_name": "lysine-specific demethylase 3B", "gene_name": "Kdm3b", "gene_names_uniprotkb": "Kdm3b; Jhdm2b; Jmjd1b; Kiaa1082", "gene_names_refseq": "5830462I21Rik; JHDM2B; Jmjd1b; Kdm3b; mKIAA1082", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SAPAEFAQENKAPFEAVKRF", "down_seq": "LDERSLACRQDSDSSTNSDL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6ZPY7", "url": "https://www.uniprot.org/uniprotkb/Q6ZPY7" } ], "site_lbl": "Ser799" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1283", "end_pos": "1283" }, { "start_pos": "388", "end_pos": "388" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "415", "end_pos": "415" }, { "start_pos": "421", "end_pos": "421" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "427", "end_pos": "427" }, { "start_pos": "655", "end_pos": "655" }, { "start_pos": "658", "end_pos": "658" }, { "start_pos": "661", "end_pos": "661" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1266", "end_pos": "1266" }, { "start_pos": "1571", "end_pos": "1571" }, { "start_pos": "269", "end_pos": "269" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "655", "end_pos": "655" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1254", "end_pos": "1254" }, { "start_pos": "1260", "end_pos": "1260" }, { "start_pos": "493", "end_pos": "493" }, { "start_pos": "547", "end_pos": "547" }, { "start_pos": "557", "end_pos": "557" }, { "start_pos": "561", "end_pos": "561" }, { "start_pos": "615", "end_pos": "615" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "774", "end_pos": "774" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "799", "end_pos": "799" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6ZPY7-1.779.779", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "A2AUC9-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "A2AUC9-1", "length": 606, "uniprot_id": "KLH41_MOUSE", "protein_name": "Kelch-like protein 41", "refseq_ac": "NP_001074556", "refseq_name": "kelch-like protein 41", "gene_name": "Klhl41", "gene_names_uniprotkb": "Klhl41; Kbtbd10", "gene_names_refseq": "Gm112; Kbtbd10; Klhl41; SARCOSIN", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "A2AUC9", "url": "https://www.uniprot.org/uniprotkb/A2AUC9" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "A reference dataset of O-GlcNAc proteins in quadriceps skeletal muscle from mice.", "journal": "Glycobiology", "date": "2025-02-10", "authors": "Jaiswal Ruchi, Liu Yimin, Petriello Michael, Zhang Xiangmin, Yi Zhengping, Fehl Charlie", "evidence": [ { "database": "O-GlcNAc Database", "id": "A2AUC9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2AUC9" } ], "reference": [ { "type": "PubMed", "id": "39927985", "url": "https://glygen.org/publication/PubMed/39927985" } ] } ], "crossref": [ { "id": "39927985", "url": "https://glygen.org/publication/PubMed/39927985", "database": "PubMed", "categories": [ "Other" ] }, { "id": "A2AUC9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2AUC9", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "39927985", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39927985" }, { "id": "A2AUC9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2AUC9" } ] } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "3", "end_pos": "3" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "A2AUC9-1.3.3", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "A2AUC9-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "A2AUC9-1", "length": 606, "uniprot_id": "KLH41_MOUSE", "protein_name": "Kelch-like protein 41", "refseq_ac": "NP_001074556", "refseq_name": "kelch-like protein 41", "gene_name": "Klhl41", "gene_names_uniprotkb": "Klhl41; Kbtbd10", "gene_names_refseq": "Gm112; Kbtbd10; Klhl41; SARCOSIN", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "A2AUC9", "url": "https://www.uniprot.org/uniprotkb/A2AUC9" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "A2AUC9", "url": "https://www.uniprot.org/uniprotkb/A2AUC9", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MD", "down_seq": "QRELAEELRLYQSTLLQDGL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "A2AUC9", "url": "https://www.uniprot.org/uniprotkb/A2AUC9" } ], "site_lbl": "Ser3" } ], "all_sites": [ { "type": "phosphorylation", "site_list": [ { "start_pos": "3", "end_pos": "3" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "A2AUC9-1.0.0", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "E0CZ16-1.356.356", "start_pos": 356, "end_pos": 356, "uniprot_canonical_ac": "E0CZ16-1", "length": 587, "uniprot_id": "KLHL3_MOUSE", "protein_name": "Kelch-like protein 3", "refseq_ac": "NP_001349344", "refseq_name": "kelch-like protein 3 isoform 1", "gene_name": "Klhl3", "gene_names_uniprotkb": "Klhl3", "gene_names_refseq": "7530408C15Rik; EG627648; Klhl3", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "GlyGen", "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889", "database": "GlyGen", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RRCRAGVVFMAGHVYAVGGF", "down_seq": "GSLRVRTVDVYDGVKDQWTS", "glycosylation": [ { "glytoucan_ac": "G29209BS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "AGVVFMAGHVYAVGGFNGSLR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn356", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000889", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000889" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "356", "end_pos": "356" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "470", "end_pos": "587" }, { "start_pos": "528", "end_pos": "528" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "433", "end_pos": "433" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "E0CZ16-1.375.375", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "E0CZ16-1.376.376", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "E0CZ16-1.470.587", "start_pos": 470, "end_pos": 587, "uniprot_canonical_ac": "E0CZ16-1", "length": 587, "uniprot_id": "KLHL3_MOUSE", "protein_name": "Kelch-like protein 3", "refseq_ac": "NP_001349344", "refseq_name": "kelch-like protein 3 isoform 1", "gene_name": "Klhl3", "gene_names_uniprotkb": "Klhl3", "gene_names_refseq": "7530408C15Rik; EG627648; Klhl3", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Generation and analysis of pseudohypoaldosteronism type II knock-in mice caused by a nonsense KLHL3 mutation in the Kelch domain.", "journal": "FASEB journal : official publication of the Federation of American Societies for Experimental Biology", "date": "2022-06", "authors": "Lin Chien-Ming, Sung Chih-Chien, Yang Sung-Sen, Chen Ying-Chuan, Huang Shih-Ming, Lin Shih-Hua", "evidence": [ { "database": "UniProtKB", "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16" }, { "database": "RefSeq", "id": "NP_001349344", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001349344" } ], "reference": [ { "type": "PubMed", "id": "35621709", "url": "https://glygen.org/publication/PubMed/35621709" } ] } ], "crossref": [ { "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "35621709", "url": "https://glygen.org/publication/PubMed/35621709", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "WIYVADMSTRRSGAGVGVLSGQLYATGGHDGPLVRKSVEVYDPGTNTWKQVADMNMCRRNAGVCAVNGLLYVVGGDDGSCNLASVEYYNPVTDKWTLLPTNMSTGRSYAGVAVIHKSL", "start_aa": "W", "up_seq": "DGASRQCLSTVEQYNPATNE", "down_seq": "", "mutagenesis": [ { "sequence_org": "WIYVADMSTRRSGAGVGVLSGQLYATGGHDGPLVRKSVEVYDPGTNTWKQVADMNMCRRNAGVCAVNGLLYVVGGDDGSCNLASVEYYNPVTDKWTLLPTNMSTGRSYAGVAVIHKSL", "sequence_mut": "", "comment": "Knockin mice display a pseudohypoaldosteronism type II (PHA2)-like phenotype, characterized by low-renin hypertension, hyperkalemia with reduced renal potassium excretion and hyperchloremic metabolic acidosis. Cells show increased levels of WNK1 and WNK4.", "evidence": [ { "database": "UniProtKB", "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16" }, { "database": "PubMed", "id": "35621709", "url": "https://glygen.org/publication/PubMed/35621709" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "356", "end_pos": "356" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "470", "end_pos": "587" }, { "start_pos": "528", "end_pos": "528" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "433", "end_pos": "433" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "E0CZ16-1.528.528", "start_pos": 528, "end_pos": 528, "uniprot_canonical_ac": "E0CZ16-1", "length": 587, "uniprot_id": "KLHL3_MOUSE", "protein_name": "Kelch-like protein 3", "refseq_ac": "NP_001349344", "refseq_name": "kelch-like protein 3 isoform 1", "gene_name": "Klhl3", "gene_names_uniprotkb": "Klhl3", "gene_names_refseq": "7530408C15Rik; EG627648; Klhl3", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Impaired degradation of WNK1 and WNK4 kinases causes PHAII in mutant KLHL3 knock-in mice.", "journal": "Human molecular genetics", "date": "2014-10-01", "authors": "Susa Koichiro, Sohara Eisei, Rai Tatemitsu, Zeniya Moko, Mori Yutaro, Mori Takayasu, Chiga Motoko, Nomura Naohiro, Nishida Hidenori, Takahashi Daiei, Isobe Kiyoshi, Inoue Yuichi, Takeishi Kenta, Takeda Naoki, Sasaki Sei, Uchida Shinichi", "evidence": [ { "database": "UniProtKB", "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16" }, { "database": "RefSeq", "id": "NP_001349344", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001349344" } ], "reference": [ { "type": "PubMed", "id": "24821705", "url": "https://glygen.org/publication/PubMed/24821705" } ] } ], "crossref": [ { "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24821705", "url": "https://glygen.org/publication/PubMed/24821705", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EVYDPGTNTWKQVADMNMCR", "down_seq": "NAGVCAVNGLLYVVGGDDGS", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "H", "comment": "Knockin mice display a pseudohypoaldosteronism type II (PHA2)-like phenotype, characterized by low-renin hypertension, hyperkalemia with reduced renal potassium excretion and hyperchloremic metabolic acidosis. Cells show increased levels of WNK1 and WNK4.", "evidence": [ { "database": "UniProtKB", "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16" }, { "database": "PubMed", "id": "24821705", "url": "https://glygen.org/publication/PubMed/24821705" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "356", "end_pos": "356" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "470", "end_pos": "587" }, { "start_pos": "528", "end_pos": "528" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "433", "end_pos": "433" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "E0CZ16-1.295.295", "start_pos": 295, "end_pos": 295, "uniprot_canonical_ac": "E0CZ16-1", "length": 587, "uniprot_id": "KLHL3_MOUSE", "protein_name": "Kelch-like protein 3", "refseq_ac": "NP_001349344", "refseq_name": "kelch-like protein 3 isoform 1", "gene_name": "Klhl3", "gene_names_uniprotkb": "Klhl3", "gene_names_refseq": "7530408C15Rik; EG627648; Klhl3", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YHLLPLDQRLLIKNPRTKPR", "down_seq": "PVSLPKVMIVVGGQAPKAIR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16" } ], "site_lbl": "Thr295" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "356", "end_pos": "356" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "470", "end_pos": "587" }, { "start_pos": "528", "end_pos": "528" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "433", "end_pos": "433" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "E0CZ16-1.375.375", "start_pos": 375, "end_pos": 375, "uniprot_canonical_ac": "E0CZ16-1", "length": 587, "uniprot_id": "KLHL3_MOUSE", "protein_name": "Kelch-like protein 3", "refseq_ac": "NP_001349344", "refseq_name": "kelch-like protein 3 isoform 1", "gene_name": "Klhl3", "gene_names_uniprotkb": "Klhl3", "gene_names_refseq": "7530408C15Rik; EG627648; Klhl3", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "FNGSLRVRTVDVYDGVKDQW", "down_seq": "SIASMQERRSTLGAAVLNDL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16" } ], "site_lbl": "Thr375" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "356", "end_pos": "356" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "470", "end_pos": "587" }, { "start_pos": "528", "end_pos": "528" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "433", "end_pos": "433" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "E0CZ16-1.356.356", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "E0CZ16-1.376.376", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "E0CZ16-1.376.376", "start_pos": 376, "end_pos": 376, "uniprot_canonical_ac": "E0CZ16-1", "length": 587, "uniprot_id": "KLHL3_MOUSE", "protein_name": "Kelch-like protein 3", "refseq_ac": "NP_001349344", "refseq_name": "kelch-like protein 3 isoform 1", "gene_name": "Klhl3", "gene_names_uniprotkb": "Klhl3", "gene_names_refseq": "7530408C15Rik; EG627648; Klhl3", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NGSLRVRTVDVYDGVKDQWT", "down_seq": "IASMQERRSTLGAAVLNDLL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16" } ], "site_lbl": "Ser376" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "356", "end_pos": "356" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "470", "end_pos": "587" }, { "start_pos": "528", "end_pos": "528" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "433", "end_pos": "433" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "E0CZ16-1.356.356", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "E0CZ16-1.375.375", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "E0CZ16-1.433.433", "start_pos": 433, "end_pos": 433, "uniprot_canonical_ac": "E0CZ16-1", "length": 587, "uniprot_id": "KLHL3_MOUSE", "protein_name": "Kelch-like protein 3", "refseq_ac": "NP_001349344", "refseq_name": "kelch-like protein 3 isoform 1", "gene_name": "Klhl3", "gene_names_uniprotkb": "Klhl3", "gene_names_refseq": "7530408C15Rik; EG627648; Klhl3", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Angiotensin II signaling via protein kinase C phosphorylates Kelch-like 3, preventing WNK4 degradation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2014", "authors": "Shibata S, Arroyo JP, Castaneda-Bueno M, Puthumana J, Zhang J, Uchida S, Stone KL, Lam TT, Lifton RP", "evidence": [ { "database": "UniProtKB", "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16" }, { "database": "iPTMnet", "id": "E0CZ16", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/E0CZ16" } ], "reference": [ { "type": "PubMed", "id": "25313067", "url": "https://glygen.org/publication/PubMed/25313067" } ] } ], "crossref": [ { "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "25313067", "url": "https://glygen.org/publication/PubMed/25313067", "database": "PubMed", "categories": [ "Other" ] }, { "id": "E0CZ16", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/E0CZ16", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AYSYKTNEWFFVAPMNTRRS", "down_seq": "VGVGVVEGKLYAVGGYDGAS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "E0CZ16", "url": "https://www.uniprot.org/uniprotkb/E0CZ16" }, { "database": "PubMed", "id": "25313067", "url": "https://glygen.org/publication/PubMed/25313067" }, { "database": "iPTMnet", "id": "E0CZ16", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/E0CZ16" } ], "site_lbl": "Ser433" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "356", "end_pos": "356" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "470", "end_pos": "587" }, { "start_pos": "528", "end_pos": "528" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "295", "end_pos": "295" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "376", "end_pos": "376" }, { "start_pos": "433", "end_pos": "433" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P41160-1.50.50", "start_pos": 50, "end_pos": 50, "uniprot_canonical_ac": "P41160-1", "length": 167, "uniprot_id": "LEP_MOUSE", "protein_name": "Leptin", "refseq_ac": "NP_032519", "refseq_name": "leptin precursor", "gene_name": "Lep", "gene_names_uniprotkb": "Lep; Ob", "gene_names_refseq": "Lep; obese; ob", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P41160", "url": "https://www.uniprot.org/uniprotkb/P41160" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "LEP O-GlcNAcylation inactivates NF-\u03baB pathway by suppressing LEP protein level and thus mediates cellular senescence and osteogenic differentiation in mouse mesenchymal stem cells.", "journal": "BMC molecular and cell biology", "date": "2024-12-18", "authors": "Zhang Zhuang, Zhou Chaoqing, Yu Lili", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "P41160", "url": "https://oglcnac.org/atlas/detail/P41160" } ], "reference": [ { "type": "PubMed", "id": "39695926", "url": "https://glygen.org/publication/PubMed/39695926" } ] } ], "crossref": [ { "id": "39695926", "url": "https://glygen.org/publication/PubMed/39695926", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P41160", "url": "https://oglcnac.org/atlas/detail/P41160", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DTKTLIKTIVTRINDISHTQ", "down_seq": "VSAKQRVTGLDFIPGLHPIL", "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "S", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser50", "evidence": [ { "id": "39695926", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39695926" }, { "id": "P41160", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P41160" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "50", "end_pos": "50" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P02469-1.1041.1041", "start_pos": 1041, "end_pos": 1041, "uniprot_canonical_ac": "P02469-1", "length": 1786, "uniprot_id": "LAMB1_MOUSE", "protein_name": "Laminin subunit beta-1", "refseq_ac": "NP_032508", "refseq_name": "laminin subunit beta-1 precursor", "gene_name": "Lamb1", "gene_names_uniprotkb": "Lamb1; Lamb-1; Lamb1-1", "gene_names_refseq": "D130003D08Rik; Lamb-1; Lamb1-1; Lamb1", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "GlyGen", "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LRQDCRKCVCNYLGTVKEHC", "down_seq": "GSDCHCDKATGQCSCLPNVI", "glycosylation": [ { "glytoucan_ac": "G42124LM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "EHCNGSDCHCDK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1041", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000889", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000889" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1041", "evidence": [ { "id": "P02469", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P02469#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1343", "end_pos": "1343" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1643", "end_pos": "1643" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "677", "end_pos": "677" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "234", "end_pos": "234" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1496", "end_pos": "1496" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P02469-1.1195.1195", "start_pos": 1195, "end_pos": 1195, "uniprot_canonical_ac": "P02469-1", "length": 1786, "uniprot_id": "LAMB1_MOUSE", "protein_name": "Laminin subunit beta-1", "refseq_ac": "NP_032508", "refseq_name": "laminin subunit beta-1 precursor", "gene_name": "Lamb1", "gene_names_uniprotkb": "Lamb1; Lamb-1; Lamb1-1", "gene_names_refseq": "D130003D08Rik; Lamb-1; Lamb1-1; Lamb1", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DCTPCHQCFALWDAIIGELT", "down_seq": "RTHKFLEKAKALKISGVIGP", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1195", "evidence": [ { "id": "P02469", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P02469#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1343", "end_pos": "1343" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1643", "end_pos": "1643" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "677", "end_pos": "677" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "234", "end_pos": "234" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1496", "end_pos": "1496" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P02469-1.120.120", "start_pos": 120, "end_pos": 120, "uniprot_canonical_ac": "P02469-1", "length": 1786, "uniprot_id": "LAMB1_MOUSE", "protein_name": "Laminin subunit beta-1", "refseq_ac": "NP_032508", "refseq_name": "laminin subunit beta-1 precursor", "gene_name": "Lamb1", "gene_names_uniprotkb": "Lamb1; Lamb-1; Lamb1-1", "gene_names_refseq": "D130003D08Rik; Lamb-1; Lamb1-1; Lamb1", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "4AQS", "url": "https://www.rcsb.org/structure/4AQS", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "4AQS|A|120", "url": "", "database": "", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "VTTFAPNRLKIWWQSENGVE", "down_seq": "VTIQLDLEAEFHFTHLIMTF", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=4AQS&bu=0&command=select+.A:120;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn120", "evidence": [ { "id": "P02469", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P02469#ptm_processing" }, { "id": "4AQS", "database": "PDB", "url": "https://www.rcsb.org/structure/4AQS" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1343", "end_pos": "1343" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1643", "end_pos": "1643" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "677", "end_pos": "677" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "234", "end_pos": "234" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1496", "end_pos": "1496" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P02469-1.122.122", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P02469-1.1279.1279", "start_pos": 1279, "end_pos": 1279, "uniprot_canonical_ac": "P02469-1", "length": 1786, "uniprot_id": "LAMB1_MOUSE", "protein_name": "Laminin subunit beta-1", "refseq_ac": "NP_032508", "refseq_name": "laminin subunit beta-1 precursor", "gene_name": "Lamb1", "gene_names_uniprotkb": "Lamb1; Lamb-1; Lamb1-1", "gene_names_refseq": "D130003D08Rik; Lamb-1; Lamb1-1; Lamb1", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "GlyGen", "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] }, { "title": "Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins.", "journal": "Nature biotechnology", "date": "2009", "authors": "Wollscheid B, Bausch-Fluck D, Henderson C, O'Brien R, Bibel M, Schiess R, Aebersold R, Watts JD", "evidence": [ { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469#ptm_processing" }, { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469" } ], "reference": [ { "type": "PubMed", "id": "19349973", "url": "https://glygen.org/publication/PubMed/19349973" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19349973", "url": "https://glygen.org/publication/PubMed/19349973", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DVTEKMAQVEVKLTDTASQS", "down_seq": "STAGELGALQAEAESLDKTV", "glycosylation": [ { "glytoucan_ac": "G92275SC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LTDTASQSNSTAGELGALQAEAESLDK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1279", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000889", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000889" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1279", "evidence": [ { "id": "P02469", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P02469#ptm_processing" }, { "id": "19349973", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19349973" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1343", "end_pos": "1343" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1643", "end_pos": "1643" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "677", "end_pos": "677" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "234", "end_pos": "234" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1496", "end_pos": "1496" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P02469-1.1336.1336", "start_pos": 1336, "end_pos": 1336, "uniprot_canonical_ac": "P02469-1", "length": 1786, "uniprot_id": "LAMB1_MOUSE", "protein_name": "Laminin subunit beta-1", "refseq_ac": "NP_032508", "refseq_name": "laminin subunit beta-1 precursor", "gene_name": "Lamb1", "gene_names_uniprotkb": "Lamb1; Lamb-1; Lamb1-1", "gene_names_refseq": "D130003D08Rik; Lamb-1; Lamb1-1; Lamb1", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Capturing site-specific heterogeneity with large-scale N-glycoproteome analysis.", "journal": "Nature communications", "date": "2019", "authors": "Riley NM, Hebert AS, Westphall MS, Coon JJ", "evidence": [ { "database": "GlyConnect", "id": "2459", "url": "https://glyconnect.expasy.org/browser/proteins/2459" } ], "reference": [ { "type": "PubMed", "id": "30899004", "url": "https://glygen.org/publication/PubMed/30899004" } ] }, { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "GlyGen", "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] }, { "title": "Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins.", "journal": "Nature biotechnology", "date": "2009", "authors": "Wollscheid B, Bausch-Fluck D, Henderson C, O'Brien R, Bibel M, Schiess R, Aebersold R, Watts JD", "evidence": [ { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469#ptm_processing" }, { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469" } ], "reference": [ { "type": "PubMed", "id": "19349973", "url": "https://glygen.org/publication/PubMed/19349973" } ] } ], "crossref": [ { "id": "30899004", "url": "https://glygen.org/publication/PubMed/30899004", "database": "PubMed", "categories": [ "Other" ] }, { "id": "2459", "url": "https://glyconnect.expasy.org/browser/proteins/2459", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19349973", "url": "https://glygen.org/publication/PubMed/19349973", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GALDSITKYFQMSLEAEKRV", "down_seq": "ASTTDPNSTVEQSALTRDRV", "glycosylation": [ { "glytoucan_ac": "G06110VR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1336", "evidence": [ { "id": "30899004", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30899004" }, { "id": "2459", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2459" } ] }, { "glytoucan_ac": "G17187PH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VNASTTDPNSTVEQSALTR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1336", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000889", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000889" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1336", "evidence": [ { "id": "P02469", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P02469#ptm_processing" }, { "id": "19349973", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19349973" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1343", "end_pos": "1343" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1643", "end_pos": "1643" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "677", "end_pos": "677" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "234", "end_pos": "234" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1496", "end_pos": "1496" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P02469-1.1343.1343", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 3 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P02469-1.1343.1343", "start_pos": 1343, "end_pos": 1343, "uniprot_canonical_ac": "P02469-1", "length": 1786, "uniprot_id": "LAMB1_MOUSE", "protein_name": "Laminin subunit beta-1", "refseq_ac": "NP_032508", "refseq_name": "laminin subunit beta-1 precursor", "gene_name": "Lamb1", "gene_names_uniprotkb": "Lamb1; Lamb-1; Lamb1-1", "gene_names_refseq": "D130003D08Rik; Lamb-1; Lamb1-1; Lamb1", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "GlyGen", "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] }, { "title": "Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins.", "journal": "Nature biotechnology", "date": "2009", "authors": "Wollscheid B, Bausch-Fluck D, Henderson C, O'Brien R, Bibel M, Schiess R, Aebersold R, Watts JD", "evidence": [ { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469#ptm_processing" }, { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469" } ], "reference": [ { "type": "PubMed", "id": "19349973", "url": "https://glygen.org/publication/PubMed/19349973" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19349973", "url": "https://glygen.org/publication/PubMed/19349973", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KYFQMSLEAEKRVNASTTDP", "down_seq": "STVEQSALTRDRVEDLMLER", "glycosylation": [ { "glytoucan_ac": "G39471UU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VNASTTDPNSTVEQSALTR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1343", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000889", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000889" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1343", "evidence": [ { "id": "P02469", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P02469#ptm_processing" }, { "id": "19349973", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19349973" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1343", "end_pos": "1343" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1643", "end_pos": "1643" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "677", "end_pos": "677" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "234", "end_pos": "234" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1496", "end_pos": "1496" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P02469-1.1336.1336", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P02469-1.1487.1487", "start_pos": 1487, "end_pos": 1487, "uniprot_canonical_ac": "P02469-1", "length": 1786, "uniprot_id": "LAMB1_MOUSE", "protein_name": "Laminin subunit beta-1", "refseq_ac": "NP_032508", "refseq_name": "laminin subunit beta-1 precursor", "gene_name": "Lamb1", "gene_names_uniprotkb": "Lamb1; Lamb-1; Lamb1-1", "gene_names_refseq": "D130003D08Rik; Lamb-1; Lamb1-1; Lamb1", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "EAKVRADEAKQNAQDVLLKT", "down_seq": "ATKEKVDKSNEDLRNLIKQI", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1487", "evidence": [ { "id": "P02469", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P02469#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1343", "end_pos": "1343" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1643", "end_pos": "1643" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "677", "end_pos": "677" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "234", "end_pos": "234" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1496", "end_pos": "1496" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "P02469-1.1496.1496", "categories": [ "phosphorylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P02469-1.1542.1542", "start_pos": 1542, "end_pos": 1542, "uniprot_canonical_ac": "P02469-1", "length": 1786, "uniprot_id": "LAMB1_MOUSE", "protein_name": "Laminin subunit beta-1", "refseq_ac": "NP_032508", "refseq_name": "laminin subunit beta-1 precursor", "gene_name": "Lamb1", "gene_names_uniprotkb": "Lamb1; Lamb-1; Lamb1-1", "gene_names_refseq": "D130003D08Rik; Lamb-1; Lamb1-1; Lamb1", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "GlyGen", "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "EAVANEVLKMEMPSTPQQLQ", "down_seq": "LTEDIRERVETLSQVEVILQ", "glycosylation": [ { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "MEMPSTPQQLQNLTEDIR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1542", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000889", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000889" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1542", "evidence": [ { "id": "P02469", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P02469#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1343", "end_pos": "1343" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1643", "end_pos": "1643" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "677", "end_pos": "677" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "234", "end_pos": "234" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1496", "end_pos": "1496" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P02469-1.1643.1643", "start_pos": 1643, "end_pos": 1643, "uniprot_canonical_ac": "P02469-1", "length": 1786, "uniprot_id": "LAMB1_MOUSE", "protein_name": "Laminin subunit beta-1", "refseq_ac": "NP_032508", "refseq_name": "laminin subunit beta-1 precursor", "gene_name": "Lamb1", "gene_names_uniprotkb": "Lamb1; Lamb-1; Lamb1-1", "gene_names_refseq": "D130003D08Rik; Lamb-1; Lamb1-1; Lamb1", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "GlyGen", "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] }, { "title": "Capturing site-specific heterogeneity with large-scale N-glycoproteome analysis.", "journal": "Nature communications", "date": "2019", "authors": "Riley NM, Hebert AS, Westphall MS, Coon JJ", "evidence": [ { "database": "GlyConnect", "id": "2459", "url": "https://glyconnect.expasy.org/browser/proteins/2459" } ], "reference": [ { "type": "PubMed", "id": "30899004", "url": "https://glygen.org/publication/PubMed/30899004" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "30899004", "url": "https://glygen.org/publication/PubMed/30899004", "database": "PubMed", "categories": [ "Other" ] }, { "id": "2459", "url": "https://glyconnect.expasy.org/browser/proteins/2459", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TQNLLTSIESETAASEETLT", "down_seq": "ASQRISKLERNVEELKRKAA", "glycosylation": [ { "glytoucan_ac": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "QADEDIQGTQNLLTSIESETAASEETLTNASQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1643", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000889", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000889" } ] }, { "glytoucan_ac": "G39188ZX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1643", "evidence": [ { "id": "30899004", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30899004" }, { "id": "2459", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/2459" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1643", "evidence": [ { "id": "P02469", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P02469#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1343", "end_pos": "1343" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1643", "end_pos": "1643" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "677", "end_pos": "677" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "234", "end_pos": "234" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1496", "end_pos": "1496" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 3 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 2 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 2 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P02469-1.356.356", "start_pos": 356, "end_pos": 356, "uniprot_canonical_ac": "P02469-1", "length": 1786, "uniprot_id": "LAMB1_MOUSE", "protein_name": "Laminin subunit beta-1", "refseq_ac": "NP_032508", "refseq_name": "laminin subunit beta-1 precursor", "gene_name": "Lamb1", "gene_names_uniprotkb": "Lamb1; Lamb-1; Lamb1-1", "gene_names_refseq": "D130003D08Rik; Lamb-1; Lamb1-1; Lamb1", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "4AQS", "url": "https://www.rcsb.org/structure/4AQS", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "4AQS|A|356", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "NCNEHSSSCHFDMAVFLATG", "down_seq": "VSGGVCDNCQHNTMGRNCEQ", "glycosylation": [ { "glytoucan_ac": "G26551VB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=4AQS&bu=0&command=select+.A:356;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn356", "evidence": [ { "id": "4AQS", "database": "PDB", "url": "https://www.rcsb.org/structure/4AQS" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn356", "evidence": [ { "id": "P02469", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P02469#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1343", "end_pos": "1343" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1643", "end_pos": "1643" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "677", "end_pos": "677" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "234", "end_pos": "234" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1496", "end_pos": "1496" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "icn3d_view.label", "icn3d_view.url", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P02469-1.519.519", "start_pos": 519, "end_pos": 519, "uniprot_canonical_ac": "P02469-1", "length": 1786, "uniprot_id": "LAMB1_MOUSE", "protein_name": "Laminin subunit beta-1", "refseq_ac": "NP_032508", "refseq_name": "laminin subunit beta-1 precursor", "gene_name": "Lamb1", "gene_names_uniprotkb": "Lamb1; Lamb-1; Lamb1-1", "gene_names_refseq": "D130003D08Rik; Lamb-1; Lamb1-1; Lamb1", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [], "crossref": [ { "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GLSNDLDGCRPCDCDLGGAL", "down_seq": "NSCSEDSGQCSCLPHMIGRQ", "glycosylation": [ { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "predicted", "site_category_dict": { "predicted": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn519", "evidence": [ { "id": "P02469", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P02469#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1343", "end_pos": "1343" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1643", "end_pos": "1643" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "677", "end_pos": "677" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "234", "end_pos": "234" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1496", "end_pos": "1496" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P02469-1.677.677", "start_pos": 677, "end_pos": 677, "uniprot_canonical_ac": "P02469-1", "length": 1786, "uniprot_id": "LAMB1_MOUSE", "protein_name": "Laminin subunit beta-1", "refseq_ac": "NP_032508", "refseq_name": "laminin subunit beta-1 precursor", "gene_name": "Lamb1", "gene_names_uniprotkb": "Lamb1; Lamb-1; Lamb1-1", "gene_names_refseq": "D130003D08Rik; Lamb-1; Lamb1-1; Lamb1", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome", "journal": "bioRxiv", "date": "2023", "authors": "Potel C.M., Burtscher M.L., Garrido-Rodriguez M., Brauer-Nikonow A., Becher I., Typas A., Zimmermann M., Savitski M.", "evidence": [ { "database": "GlyGen", "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889" } ], "reference": [ { "type": "DOI", "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" } ] } ], "crossref": [ { "id": "10.1101/2023.09.13.557529", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529", "database": "DOI", "categories": [ "Other" ] }, { "id": "GLY_000889", "url": "https://data.glygen.org/GLY_000889", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LSPGSRYVVLPRPVCFEKGM", "down_seq": "YTVRLELPQYTASGSDVESP", "glycosylation": [ { "glytoucan_ac": "G41247ZX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GMNYTVR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn677", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000889", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000889" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn677", "evidence": [ { "id": "P02469", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P02469#ptm_processing" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1343", "end_pos": "1343" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1643", "end_pos": "1643" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "677", "end_pos": "677" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "234", "end_pos": "234" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1496", "end_pos": "1496" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P02469-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P02469-1", "length": 1786, "uniprot_id": "LAMB1_MOUSE", "protein_name": "Laminin subunit beta-1", "refseq_ac": "NP_032508", "refseq_name": "laminin subunit beta-1 precursor", "gene_name": "Lamb1", "gene_names_uniprotkb": "Lamb1; Lamb-1; Lamb1-1", "gene_names_refseq": "D130003D08Rik; Lamb-1; Lamb1-1; Lamb1", "species": [ { "name": "Mus musculus", "taxid": 10090, "evidence": [ { "database": "UniProtKB", "id": "P02469", "url": "https://www.uniprot.org/uniprotkb/P02469" } ], "common_name": "Mouse", "glygen_name": "Mouse", "reference_species": "Mus musculus [10090]" } ], "publication": [ { "title": "A reference dataset of O-GlcNAc proteins in quadriceps skeletal muscle from mice.", "journal": "Glycobiology", "date": "2025-02-10", "authors": "Jaiswal Ruchi, Liu Yimin, Petriello Michael, Zhang Xiangmin, Yi Zhengping, Fehl Charlie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P02469", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P02469" } ], "reference": [ { "type": "PubMed", "id": "39927985", "url": "https://glygen.org/publication/PubMed/39927985" } ] }, { "title": "Differential Detection of O-GlcNAcylated proteins in the heart using antibodies.", "journal": "Analytical biochemistry", "date": "2023-10-01", "authors": "Narayanan Bhargavi, Zahra Fiddia, Reeves Russell A, Aggarwal Akanksha, O'Meally Robert N, Henry Roger K, Craven Megan, Jacobson Avital, Cole Robert N, Kohr Mark J, Umapathi Priya, Zachara Natasha E", "evidence": [ { "database": "O-GlcNAc Database", "id": "P02469", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P02469" } ], "reference": [ { "type": "PubMed", "id": "37507081", "url": "https://glygen.org/publication/PubMed/37507081" } ] } ], "crossref": [ { "id": "39927985", "url": "https://glygen.org/publication/PubMed/39927985", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P02469", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P02469", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "37507081", "url": "https://glygen.org/publication/PubMed/37507081", "database": "PubMed", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "39927985", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39927985" }, { "id": "P02469", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P02469" }, { "id": "37507081", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37507081" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1041", "end_pos": "1041" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "1279", "end_pos": "1279" }, { "start_pos": "1336", "end_pos": "1336" }, { "start_pos": "1343", "end_pos": "1343" }, { "start_pos": "1487", "end_pos": "1487" }, { "start_pos": "1542", "end_pos": "1542" }, { "start_pos": "1643", "end_pos": "1643" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "677", "end_pos": "677" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "234", "end_pos": "234" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1496", "end_pos": "1496" }, { "start_pos": "1666", "end_pos": "1666" }, { "start_pos": "250", "end_pos": "250" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] } ]